Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 102 of 160
Found at i:19334017 original size:543 final size:543
Alignment explanation
Indices: 19332987--19334084 Score: 1603
Period size: 543 Copynumber: 2.0 Consensus size: 543
19332977 ATGCCCTTAC
*
19332987 ATAAAAGACTAGCTAATCTATAACGATCCTAATTCAAAAAATATTCACACTCATACTCATGTGGT
1 ATAAAAGACTAGCTAATCTATAACGATCCTAATTCAAAAAATATTCACACTCATACCCATGTGGT
** *
19333052 TCATCTCATTCTCTTTTAATCTACTTGCAAACATTAAACATTCATCATACCTGTAGATCTTCTCA
66 TCATCTCATTCTCTTTTAATCTACTCACAAACATTAAACAATCATCATACCTGTAGATCTTCTCA
* * * *
19333117 ATCTCCTCTAATCCTATGGAATATTTTCACATCAAACAATAAAACATACACACCTATAAGGACTC
131 ATCTCCTCTAATCATATGGAATATTCTCACATCAAACAACAAAACATACACACCTATAAAGACTC
* * * *
19333182 TTTCAATCTCTTCTAATCCTATGGAGTGTCTATCCGATAAAACCTTACAACTCTTTTTACATCTT
196 TTTCAATCACTTCTAATCCTATGGAGTGTCTATCCAATAAAACCTAACAACTCATTTTACATCTT
* ** * * * *
19333247 TCTCTCATGCCTAATCCTATAAAAACTTTGACTATTTATAAGCCTACTAACTTATCTTCCAAGAA
261 TCTCTCATACCTAATCCTATAAAAACTTCAACTATTTATAAACCTACTAACTTACCTACCAAAAA
19333312 TCTCTTTTCTTTTATAATTCTTCACTTGAAAGTCTATTTTCCATCAAGTATTATCTAACCAATTT
326 TCTCTTTTCTTTTATAATTCTTCACTTGAAAGTCTATTTTCCATCAAGTATTATCTAACCAATTT
* * *
19333377 TGAAAAAATATCAACCAAATCTCTTGTGAAATTTGAATCACCATTTCTAACATATGTATCCGTTT
391 TGAAAAAATATCAACCAAATCTCTTATGAAATTTGAATCACCATTTCTAACACATGTATCAGTTT
* ** * * *
19333442 TGTCATATTAGGTTGAACAAAAAATTAAAATGCCCAGACCAACCAAATAACTAGATTGCCTTTGA
456 TATCATATTAGGTCAAACAAAAAATGAAAATGCCCAAACCAACCAAATAACTAGAGTGCCTTTGA
19333507 GATCCTAAACTATTTTCAAATAA
521 GATCCTAAACTATTTTCAAATAA
* * * *
19333530 ATAAAAGACTAGCTAATCTCTAACGATCCTAATTTAGATAATATTCACACTCATACCCATGTGGT
1 ATAAAAGACTAGCTAATCTATAACGATCCTAATTCAAAAAATATTCACACTCATACCCATGTGGT
*
19333595 TCATCTCATTCTCTTTTAATCTACTCACAAACATTAAACAATCATCATA-TTCGTAGATGC-TCT
66 TCATCTCATTCTCTTTTAATCTACTCACAAACATTAAACAATCATCATACCT-GTAGAT-CTTCT
* * * * *
19333658 CAATCTTCTTTAGTCATATGGAGTATTCTCACATCAAACAACAAAATATACACACCTATAAAGAC
129 CAATCTCCTCTAATCATATGGAATATTCTCACATCAAACAACAAAACATACACACCTATAAAGAC
* * * * * *
19333723 TCTTTCAATCACTTTTAGTCCTAT-GAGGTGTCTATCTAATAAAACCTAATAATTCATTTTATAT
194 TCTTTCAATCACTTCTAATCCTATGGA-GTGTCTATCCAATAAAACCTAACAACTCATTTTACAT
* * * * *
19333787 CTTTTTCTTATACCTAATCTTAT-AAAACTTCAATTATTTATAAACTTACTAACTTACCTACCAA
258 CTTTCTCTCATACCTAATCCTATAAAAACTTCAACTATTTATAAACCTACTAACTTACCTACCAA
* * * *
19333851 AAATCTCTTTTCTTTTATAATTCTTCATTTGAAAGTCTTTTTTTCCGTCAAGTATTATCTAATCA
323 AAATCTCTTTTCTTTTATAATTCTTCACTTGAAAGTC-TATTTTCCATCAAGTATTATCTAACCA
* *
19333916 ATTTTGAAAAAATATTAACCAAATCTCTTATGAAATTTGAATCACTATTTCTAACACATGTAAT-
387 ATTTTGAAAAAATATCAACCAAATCTCTTATGAAATTTGAATCACCATTTCTAACACATGT-ATC
*
19333980 AGTTTTATCATATTAGGTCAAACAAAAAATGAAAATGCCCAAACCGACCAAATAACTAGAGTGCC
451 AGTTTTATCATATTAGGTCAAACAAAAAATGAAAATGCCCAAACCAACCAAATAACTAGAGTGCC
19334045 TTTGAGATCCTAAACTATTTTCAAATAA
516 TTTGAGATCCTAAACTATTTTCAAATAA
19334073 ATAAAAAGACTA
1 AT-AAAAGACTA
19334085 TTTCACTCCT
Statistics
Matches: 493, Mismatches: 56, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
542 72 0.15
543 409 0.83
544 12 0.02
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (543 bp):
ATAAAAGACTAGCTAATCTATAACGATCCTAATTCAAAAAATATTCACACTCATACCCATGTGGT
TCATCTCATTCTCTTTTAATCTACTCACAAACATTAAACAATCATCATACCTGTAGATCTTCTCA
ATCTCCTCTAATCATATGGAATATTCTCACATCAAACAACAAAACATACACACCTATAAAGACTC
TTTCAATCACTTCTAATCCTATGGAGTGTCTATCCAATAAAACCTAACAACTCATTTTACATCTT
TCTCTCATACCTAATCCTATAAAAACTTCAACTATTTATAAACCTACTAACTTACCTACCAAAAA
TCTCTTTTCTTTTATAATTCTTCACTTGAAAGTCTATTTTCCATCAAGTATTATCTAACCAATTT
TGAAAAAATATCAACCAAATCTCTTATGAAATTTGAATCACCATTTCTAACACATGTATCAGTTT
TATCATATTAGGTCAAACAAAAAATGAAAATGCCCAAACCAACCAAATAACTAGAGTGCCTTTGA
GATCCTAAACTATTTTCAAATAA
Found at i:19335532 original size:22 final size:22
Alignment explanation
Indices: 19335507--19335554 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
19335497 TTTTTATTTT
*
19335507 TTATTATAAAATTTTTAAAATA
1 TTATTATAAAAATTTTAAAATA
*
19335529 TTATTATAAAAATTTTAAATTA
1 TTATTATAAAAATTTTAAAATA
19335551 TTAT
1 TTAT
19335555 AACGTATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATTATAAAAATTTTAAAATA
Found at i:19336291 original size:56 final size:57
Alignment explanation
Indices: 19336202--19336310 Score: 157
Period size: 56 Copynumber: 1.9 Consensus size: 57
19336192 AATATTTTTT
* * * *
19336202 ATTTATTATAAGAAAAAAATTAATATTTTAACTTTTTTCTCGATTGACTTTATATAA
1 ATTTATTAGAAGAAAAAAATTAATATTTCAACTTTTTCCTCAATTGACTTTATATAA
* *
19336259 ATTTATTAGAAG-AAAAAATTGATATTTCAACTTTTTCCTCAATTGATTTTAT
1 ATTTATTAGAAGAAAAAAATTAATATTTCAACTTTTTCCTCAATTGACTTTAT
19336311 TTATTTTATT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
56 35 0.76
57 11 0.24
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (57 bp):
ATTTATTAGAAGAAAAAAATTAATATTTCAACTTTTTCCTCAATTGACTTTATATAA
Found at i:19337885 original size:44 final size:44
Alignment explanation
Indices: 19337814--19337939 Score: 128
Period size: 44 Copynumber: 2.9 Consensus size: 44
19337804 TTTTTTTTAT
* * * *
19337814 ACTTCTCCAAGCAGAGACTTGGT-AACTTTTTGAAACTTCAAAAA
1 ACTTCTCTAAACAGAGGCTT-GTCAACTTTTTGAAAATTCAAAAA
** *
19337858 ACTTCTCTAAACAGAGGCTTGTCAACTTTTTGAAAATTTGAAAG
1 ACTTCTCTAAACAGAGGCTTGTCAACTTTTTGAAAATTCAAAAA
* * * * *
19337902 ACTTTTCTAAATAGAAGCTTGCCAACATTTTGAAAATT
1 ACTTCTCTAAACAGAGGCTTGTCAACTTTTTGAAAATT
19337940 TGGAAAGCTC
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
43 2 0.03
44 67 0.97
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.33
Consensus pattern (44 bp):
ACTTCTCTAAACAGAGGCTTGTCAACTTTTTGAAAATTCAAAAA
Found at i:19337940 original size:44 final size:45
Alignment explanation
Indices: 19337858--19337990 Score: 130
Period size: 44 Copynumber: 3.0 Consensus size: 45
19337848 ACTTCAAAAA
* * *
19337858 ACTTCTCTAAACAGAGGCTTGTCAACTTTTTGAAAATTT-GAAAG
1 ACTTCTCTAAACAGAAGCTTGCCAACATTTTGAAAATTTGGAAAG
* *
19337902 ACTTTTCTAAATAGAAGCTTGCCAACATTTTGAAAATTTGGAAAG
1 ACTTCTCTAAACAGAAGCTTGCCAACATTTTGAAAATTTGGAAAG
* ** **
19337947 -C-TCATTTAAACA-AAGGCTTAACAATTTTTTGAAAATTTGGAAAG
1 ACTTC-TCTAAACAGAA-GCTTGCCAACATTTTGAAAATTTGGAAAG
19337991 CTCCTCCAAA
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
43 3 0.04
44 66 0.89
45 5 0.07
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.34
Consensus pattern (45 bp):
ACTTCTCTAAACAGAAGCTTGCCAACATTTTGAAAATTTGGAAAG
Found at i:19338404 original size:124 final size:124
Alignment explanation
Indices: 19338010--19338485 Score: 421
Period size: 124 Copynumber: 3.9 Consensus size: 124
19338000 ATGGAGGCTC
* * *
19338010 GACAACTTTAAAAGTTTAAAAAG-TCCTTTAAACAGAGGCTTAAAAAATTTGAAAACTCTTCTAA
1 GACAACTTTAAAAATTTGAAAAGCTCCTTTAAACAGAGGCTCAAAAAATTTGAAAACTCTTCTAA
* * * *
19338074 ACAAATGCTCAATAACTTTAAAATGCTCATATAAAAAAGGCTCTTTTAAA-AAAG-GTGT
66 ACAAAGGCTCAATAACTTTTAAATTCTCATATAAAAAAGGCTCTTTTAAATAAAGACT-T
** * * * * **
19338132 GATGACTTTAAAAATTTGAAAACCT-CTTCTAAATAGTGGTTCAAAAAATCTT-AAAGTTCCTT-
1 GACAACTTTAAAAATTTGAAAAGCTCCTT-TAAACAGAGGCTCAAAAAAT-TTGAAAACT-CTTC
* ** * * * *
19338194 TTAACAAAGATTCAATAACTTTTAAATTTTCATGTGAAAAAGGCTCTTTTAAATAAA-AGCTA
63 TAAACAAAGGCTCAATAACTTTTAAATTCTCATATAAAAAAGGCTCTTTTAAATAAAGA-CTT
* ** * **
19338256 GACAACTTTAGAAATTTGGTAAGCTCCTTTAAACAAAGGCTCAAAGTATTTGAAAACTCTTCTAA
1 GACAACTTTAAAAATTTGAAAAGCTCCTTTAAACAGAGGCTCAAAAAATTTGAAAACTCTTCTAA
* * * *
19338321 ACAGAGGCTCAACAACTTTTAAATTCTCAT-TCTAAAAATGCTCTTTTAAATAAAGACTT
66 ACAAAGGCTCAATAACTTTTAAATTCTCATAT-AAAAAAGGCTCTTTTAAATAAAGACTT
* * * * ** *
19338380 GACAACTTTAAAAATTTGAAAAGCTTCTCTAAATAGAGACTTGAAAAATCT-AAAAGCTCTTCTA
1 GACAACTTTAAAAATTTGAAAAGCTCCTTTAAACAGAGGCTCAAAAAATTTGAAAA-CTCTTCTA
* ** * * *
19338444 AATAAAGGCTTGACAGCTTTAAAATTCTCATATAAAAAAGGC
65 AACAAAGGCTCAATAACTTTTAAATTCTCATATAAAAAAGGC
19338486 CCAACTACTT
Statistics
Matches: 274, Mismatches: 66, Indels: 26
0.75 0.18 0.07
Matches are distributed among these distances:
122 21 0.08
123 75 0.27
124 172 0.63
125 6 0.02
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (124 bp):
GACAACTTTAAAAATTTGAAAAGCTCCTTTAAACAGAGGCTCAAAAAATTTGAAAACTCTTCTAA
ACAAAGGCTCAATAACTTTTAAATTCTCATATAAAAAAGGCTCTTTTAAATAAAGACTT
Found at i:19338436 original size:33 final size:34
Alignment explanation
Indices: 19338384--19338456 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 34
19338374 AGACTTGACA
* * *
19338384 ACTTTAAAAATTTGAAAAGCT-TCTCTAAATAGAG
1 ACTTGAAAAATCTGAAAAGCTCT-TCTAAATAAAG
19338418 ACTTGAAAAATCT-AAAAGCTCTTCTAAATAAAG
1 ACTTGAAAAATCTGAAAAGCTCTTCTAAATAAAG
*
19338451 GCTTGA
1 ACTTGA
19338457 CAGCTTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
33 22 0.65
34 12 0.35
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (34 bp):
ACTTGAAAAATCTGAAAAGCTCTTCTAAATAAAG
Found at i:19344425 original size:18 final size:19
Alignment explanation
Indices: 19344392--19344429 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
19344382 TAGGTTATTC
19344392 TGACTTTTGTCTTTCTCTT
1 TGACTTTTGTCTTTCTCTT
19344411 TGACTTTTG-CTTTCTCTT
1 TGACTTTTGTCTTTCTCTT
19344429 T
1 T
19344430 CTTAGCTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.05, C:0.21, G:0.11, T:0.63
Consensus pattern (19 bp):
TGACTTTTGTCTTTCTCTT
Found at i:19350584 original size:40 final size:40
Alignment explanation
Indices: 19350514--19350590 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 40
19350504 AAAAAATCAT
* *
19350514 AAAAATAATAAAACTATAAAACTATATAAAAAATTAAGCA
1 AAAAATAAAAAAAATATAAAACTATATAAAAAATTAAGCA
* * *
19350554 AAAAATGAAAAAAAATA-AAAATTATGTAAAAATTTAA
1 AAAAAT-AAAAAAAATATAAAACTATATAAAAAATTAA
19350591 AAATGGCTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 23 0.74
41 8 0.26
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.23
Consensus pattern (40 bp):
AAAAATAAAAAAAATATAAAACTATATAAAAAATTAAGCA
Found at i:19355377 original size:10 final size:10
Alignment explanation
Indices: 19355362--19355400 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
19355352 CCATCAGGGA
19355362 ATTTTTTTGG
1 ATTTTTTTGG
*
19355372 ATTTTTTTTGA
1 A-TTTTTTTGG
19355383 ATTTTTTTGG
1 ATTTTTTTGG
*
19355393 GTTTTTTT
1 ATTTTTTT
19355401 TTGGTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.10, C:0.00, G:0.15, T:0.74
Consensus pattern (10 bp):
ATTTTTTTGG
Found at i:19355408 original size:10 final size:11
Alignment explanation
Indices: 19355363--19355410 Score: 62
Period size: 11 Copynumber: 4.5 Consensus size: 11
19355353 CATCAGGGAA
19355363 TTTTTTTGGAT
1 TTTTTTTGGAT
*
19355374 TTTTTTTGAAT
1 TTTTTTTGGAT
* *
19355385 TTTTTTGGGTT
1 TTTTTTTGGAT
19355396 TTTTTTTGG-T
1 TTTTTTTGGAT
19355406 TTTTT
1 TTTTT
19355411 GAAGAACTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
10 6 0.19
11 26 0.81
ACGTcount: A:0.06, C:0.00, G:0.17, T:0.77
Consensus pattern (11 bp):
TTTTTTTGGAT
Found at i:19355410 original size:21 final size:21
Alignment explanation
Indices: 19355360--19355401 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
19355350 AACCATCAGG
19355360 GAATTTTTTTGGATTTTTTTT
1 GAATTTTTTTGGATTTTTTTT
*
19355381 GAATTTTTTTGGGTTTTTTTT
1 GAATTTTTTTGGATTTTTTTT
19355402 TGGTTTTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.12, C:0.00, G:0.17, T:0.71
Consensus pattern (21 bp):
GAATTTTTTTGGATTTTTTTT
Found at i:19358996 original size:5 final size:5
Alignment explanation
Indices: 19358986--19359015 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
19358976 GGGGCAAATA
*
19358986 TTTTC TTTTC TTTTC TTTTC TTTTC ATTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
19359016 CATGCATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:19366054 original size:17 final size:17
Alignment explanation
Indices: 19366028--19366061 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
19366018 TGCTTAATTC
19366028 TAAAAAAAAACAAAAAA
1 TAAAAAAAAACAAAAAA
*
19366045 TAAAACAAAACAAAAAA
1 TAAAAAAAAACAAAAAA
19366062 AAGAGAAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.85, C:0.09, G:0.00, T:0.06
Consensus pattern (17 bp):
TAAAAAAAAACAAAAAA
Found at i:19367331 original size:120 final size:118
Alignment explanation
Indices: 19367188--19367633 Score: 400
Period size: 120 Copynumber: 3.7 Consensus size: 118
19367178 TTTCATCCCG
* * *
19367188 ATCATTTATTTTCGACCTCGACTCAGTCCTAGTCGCTTTTATTTTGGCTTGTGATTTTGTCTCGA
1 ATCATTTATTTTCGACCTCGACTC-GTCCTGGTCGCTTTTATTTTGACTTGTGATTTTATC-CGA
* * *
19367253 TCATTTGATCTTAGCTTAGTCCAGATCAATTTTTTTTATTCATGGCTTTGTCTCA
64 TCATTTGATCTTGGCTCAGTCCAGATCAATTTTTTTGATTCATGGCTTTGTCTCA
* * * * *
19367308 ATCATTTATTTTTGACCTTGACTCGTCCTGGTCAC-TTTATTTCGATTTGTGATTTTATCCTGAT
1 ATCATTTATTTTCGACCTCGACTCGTCCTGGTCGCTTTTATTTTGACTTGTGATTTTATCC-GAT
* * * * * * *
19367372 CACTTGATCTTGGCTCAGTCTAGATCAATTCTTATGATTCGTGG-TTTCATCTCG
65 CATTTGATCTTGGCTCAGTCCAGATCAATTTTTTTGATTCATGGCTTT-GTCTCA
* * * * ** *
19367426 ATCATTTATTTTCAACCTCGACACGATCCTGGTTGTTTTTATTTTGACTCAT-AGTTTAATCCCG
1 ATCATTTATTTTCGACCTCGACTCG-TCCTGGTCGCTTTTATTTTGACTTGTGA-TTTTAT-CCG
* * ** *
19367490 ATCATTTGATCTTGGCTCAATCCATATC-ATTTCTTTTGATTCATGGCTCCGTCCCA
63 ATCATTTGATCTTGGCTCAGTCCAGATCAATTT-TTTTGATTCATGGCTTTGTCTCA
* * * * * * *
19367546 ATCATTTATTTTCGATCTTGACTTGATCCTGGTCAC-TTTATTTTGA-TTCATGGTTTCATCCTG
1 ATCATTTATTTTCGACCTCGACTCG-TCCTGGTCGCTTTTATTTTGACTT-GTGATTTTATCC-G
* *
19367609 ATCACTTGATCTTGGCTCAATCCAG
63 ATCATTTGATCTTGGCTCAGTCCAG
19367634 TTCATTTCTT
Statistics
Matches: 260, Mismatches: 55, Indels: 23
0.77 0.16 0.07
Matches are distributed among these distances:
117 4 0.02
118 87 0.33
119 61 0.23
120 105 0.40
121 3 0.01
ACGTcount: A:0.19, C:0.22, G:0.15, T:0.45
Consensus pattern (118 bp):
ATCATTTATTTTCGACCTCGACTCGTCCTGGTCGCTTTTATTTTGACTTGTGATTTTATCCGATC
ATTTGATCTTGGCTCAGTCCAGATCAATTTTTTTGATTCATGGCTTTGTCTCA
Found at i:19367468 original size:238 final size:238
Alignment explanation
Indices: 19367071--19367654 Score: 701
Period size: 238 Copynumber: 2.5 Consensus size: 238
19367061 TTTCATCTTG
* * * * * * *
19367071 ATCATTTATTTTGGACCTTGATTCGATCCTAGTCACTTCATTTGACTTATGGTTTCGTCCCGATC
1 ATCATTTATTTTCGACCTTGACTCGATCCTGGTCACTTTATTTGATTTATGGTTTCATCCTGATC
* * **
19367136 ACATGATCTTGGATCAATCCAGATCATTTCTT-TGATTCGTTATTTCATCCCGATCATTTATTTT
66 ACTTGATCTTGGCTCAATCCAGATCATTTCTTATGATTCGTGGTTTCATCCCGATCATTTATTTT
* * * ** ** *
19367200 CGACCTCGACTCAGTCCTAGTCGCTTTTATTTTGGCTTGT-GATTTTGTCTCGATCATTTGATCT
131 CAACCTCGACACAGTCCTAGTCGCTTTTATTTTGACTCATAG-TTTAATCCCGATCATTTGATCT
* * * ** *
19367264 TAGCTTAGTCCAGATCAATTT-TTTTTATTCATGGCTTTGTCTCA
195 TAGCTCAATCCAGATC-ATTTCTTTTGATTCATGGCTCCGTCCCA
* * * *
19367308 ATCATTTATTTTTGACCTTGACTCG-TCCTGGTCACTTTATTTCGATTTGTGATTTTATCCTGAT
1 ATCATTTATTTTCGACCTTGACTCGATCCTGGTCACTTTATTT-GATTTATGGTTTCATCCTGAT
* * * *
19367372 CACTTGATCTTGGCTCAGTCTAGATCAATTCTTATGATTCGTGGTTTCATCTCGATCATTTATTT
65 CACTTGATCTTGGCTCAATCCAGATCATTTCTTATGATTCGTGGTTTCATCCCGATCATTTATTT
* * *
19367437 TCAACCTCGACAC-GATCCTGGTTGTTTTTATTTTGACTCATAGTTTAATCCCGATCATTTGATC
130 TCAACCTCGACACAG-TCCTAGTCGCTTTTATTTTGACTCATAGTTTAATCCCGATCATTTGATC
* *
19367501 TTGGCTCAATCCATATCATTTCTTTTGATTCATGGCTCCGTCCCA
194 TTAGCTCAATCCAGATCATTTCTTTTGATTCATGGCTCCGTCCCA
* * *
19367546 ATCATTTATTTTCGATCTTGACTTGATCCTGGTCACTTTATTTTGATTCATGGTTTCATCCTGAT
1 ATCATTTATTTTCGACCTTGACTCGATCCTGGTCACTTTA-TTTGATTTATGGTTTCATCCTGAT
* *
19367611 CACTTGATCTTGGCTCAATCCAGTTCATTTCTTATGATTTGTGG
65 CACTTGATCTTGGCTCAATCCAGATCATTTCTTATGATTCGTGG
19367655 CTCTATCCTA
Statistics
Matches: 291, Mismatches: 49, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
236 15 0.05
237 71 0.24
238 131 0.45
239 71 0.24
240 3 0.01
ACGTcount: A:0.19, C:0.21, G:0.15, T:0.45
Consensus pattern (238 bp):
ATCATTTATTTTCGACCTTGACTCGATCCTGGTCACTTTATTTGATTTATGGTTTCATCCTGATC
ACTTGATCTTGGCTCAATCCAGATCATTTCTTATGATTCGTGGTTTCATCCCGATCATTTATTTT
CAACCTCGACACAGTCCTAGTCGCTTTTATTTTGACTCATAGTTTAATCCCGATCATTTGATCTT
AGCTCAATCCAGATCATTTCTTTTGATTCATGGCTCCGTCCCA
Found at i:19367674 original size:119 final size:119
Alignment explanation
Indices: 19367014--19367694 Score: 516
Period size: 119 Copynumber: 5.7 Consensus size: 119
19367004 TTTTCACTTC
* * * *
19367014 GATCACTTGATCTTGGCTCAGTCCTA-ATCATTTCTTATGATTTGTGG-TTTCATCTTGATCATT
1 GATCACTTGATCTTGGCTCAATCC-AGATCATTTCTTATGATTCGTGGCTTTCATCCTAATCATT
* * * * *
19367077 TATTTTGGACCTTGA-TTCGATCCTAGTCACTTCA-TTTGACTTATGGTTTCGTCCC
65 TATTTTCGACCTTGACTT-GATCCTGGTCACTTTATTTTGA-TTATGGTTTCATCCT
* * ** **
19367132 GATCACATGATCTTGGATCAATCCAGATCATTTCTT-TGATTCGT-TATTTCATCCCGATCATTT
1 GATCACTTGATCTTGGCTCAATCCAGATCATTTCTTATGATTCGTGGCTTTCATCCTAATCATTT
* * * * * * * **
19367195 ATTTTCGACCTCGAC-TCAGTCCTAGTCGCTTTTATTTTGGCTTGTGATTTTGT-CT
66 ATTTTCGACCTTGACTTGA-TCCTGGTCAC-TTTATTTT-GATTATGGTTTCATCCT
* * * * * * * *
19367250 CGATCATTTGATCTTAGCTTAGTCCAGATCAATTT-TTTTTATTCATGGCTTT-GT-CTCAATCA
1 -GATCACTTGATCTTGGCTCAATCCAGATC-ATTTCTTATGATTCGTGGCTTTCATCCT-AATCA
* * * *
19367312 TTTATTTTTGACCTTGACTCG-TCCTGGTCACTTTATTTCGATT-TGTGATTTTATCCT
63 TTTATTTTCGACCTTGACTTGATCCTGGTCACTTTATTTTGATTATG-G-TTTCATCCT
* * * *
19367369 GATCACTTGATCTTGGCTCAGTCTAGATCAATTCTTATGATTCGTGG-TTTCAT-CTCGATCATT
1 GATCACTTGATCTTGGCTCAATCCAGATCATTTCTTATGATTCGTGGCTTTCATCCT-AATCATT
* * ** *** * * * *
19367432 TATTTTCAACCTCGACACGATCCTGGTTGTTTTTATTTTGACTCATAGTTTAATCCC
65 TATTTTCGACCTTGACTTGATCCTGG-TCACTTTATTTTGA-TTATGGTTTCATCCT
* * * * * * *
19367489 GATCATTTGATCTTGGCTCAATCCATATCATTTCTTTTGATTCATGGC-TCCGTCCCAATCATTT
1 GATCACTTGATCTTGGCTCAATCCAGATCATTTCTTATGATTCGTGGCTTTCATCCTAATCATTT
*
19367553 ATTTTCGATCTTGACTTGATCCTGGTCACTTTATTTTGATTCATGGTTTCATCCT
66 ATTTTCGACCTTGACTTGATCCTGGTCACTTTATTTTGATT-ATGGTTTCATCCT
* * *
19367608 GATCACTTGATCTTGGCTCAATCCAGTTCATTTCTTATGATTTGTGGCTCT-ATCCTAATCATTT
1 GATCACTTGATCTTGGCTCAATCCAGATCATTTCTTATGATTCGTGGCTTTCATCCTAATCATTT
* *
19367672 ATTCTT-GGCCTCGACTTGATCCT
66 ATT-TTCGACCTTGACTTGATCCT
19367695 ATGCATTTCA
Statistics
Matches: 438, Mismatches: 98, Indels: 53
0.74 0.17 0.09
Matches are distributed among these distances:
116 3 0.01
117 54 0.12
118 108 0.25
119 145 0.33
120 121 0.28
121 6 0.01
122 1 0.00
ACGTcount: A:0.19, C:0.22, G:0.15, T:0.45
Consensus pattern (119 bp):
GATCACTTGATCTTGGCTCAATCCAGATCATTTCTTATGATTCGTGGCTTTCATCCTAATCATTT
ATTTTCGACCTTGACTTGATCCTGGTCACTTTATTTTGATTATGGTTTCATCCT
Found at i:19367894 original size:26 final size:26
Alignment explanation
Indices: 19367858--19367935 Score: 86
Period size: 26 Copynumber: 3.0 Consensus size: 26
19367848 TTTTGGCTGG
*
19367858 GCCTAATTGGGCCCATTTTGGTCAAA
1 GCCTAACTGGGCCCATTTTGGTCAAA
*
19367884 GCCTAACTGGGCCTATTTTGGTC-AA
1 GCCTAACTGGGCCCATTTTGGTCAAA
* ***
19367909 GCCCAACTATACGCCATTTTGGTCAAA
1 GCCTAACTGGGC-CCATTTTGGTCAAA
19367936 CCCATTATGA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
25 10 0.23
26 31 0.72
27 2 0.05
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (26 bp):
GCCTAACTGGGCCCATTTTGGTCAAA
Found at i:19367985 original size:3 final size:3
Alignment explanation
Indices: 19367971--19368003 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
19367961 TTAGATACTT
19367971 TTA TTA TT- TTA TTA TTA TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19368004 TTTTTTCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
TTA
Found at i:19368422 original size:12 final size:12
Alignment explanation
Indices: 19368405--19368434 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
19368395 ACTATCTAGA
19368405 AATTTTTTTTGG
1 AATTTTTTTTGG
19368417 AATTTTTTTTGG
1 AATTTTTTTTGG
19368429 -ATTTTT
1 AATTTTT
19368435 CTAGGTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.33
12 12 0.67
ACGTcount: A:0.17, C:0.00, G:0.13, T:0.70
Consensus pattern (12 bp):
AATTTTTTTTGG
Found at i:19368790 original size:20 final size:20
Alignment explanation
Indices: 19368765--19368806 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
19368755 ATGGTAAGCC
* *
19368765 AAGATCCGCATGTTGACCAG
1 AAGATCCACACGTTGACCAG
*
19368785 AAGATCCACGCGTTGACCAG
1 AAGATCCACACGTTGACCAG
19368805 AA
1 AA
19368807 AATTCGCGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (20 bp):
AAGATCCACACGTTGACCAG
Found at i:19375638 original size:12 final size:11
Alignment explanation
Indices: 19375615--19375656 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
19375605 AAATTTACTA
19375615 GTATTTTTTTG
1 GTATTTTTTTG
19375626 GTATTTTTGTTG
1 GTATTTTT-TTG
*
19375638 GTATTTCTTTG
1 GTATTTTTTTG
*
19375649 GTGTTTTT
1 GTATTTTT
19375657 GCTAGTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.07, C:0.02, G:0.21, T:0.69
Consensus pattern (11 bp):
GTATTTTTTTG
Found at i:19375641 original size:23 final size:23
Alignment explanation
Indices: 19375612--19375666 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
19375602 GATAAATTTA
*
19375612 CTAGTATTTTTTTGGTATTTTTG
1 CTAGTATTTCTTTGGTATTTTTG
* * *
19375635 TTGGTATTTCTTTGGTGTTTTTG
1 CTAGTATTTCTTTGGTATTTTTG
19375658 CTAGTATTT
1 CTAGTATTT
19375667 ATTTCTTGAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.11, C:0.05, G:0.20, T:0.64
Consensus pattern (23 bp):
CTAGTATTTCTTTGGTATTTTTG
Found at i:19375737 original size:23 final size:23
Alignment explanation
Indices: 19375711--19375755 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
19375701 GATAAATTTA
19375711 CTAGTATTTCTTTGGTATTTTTG
1 CTAGTATTTCTTTGGTATTTTTG
* *
19375734 CTAGTGTTTCTTTGGTGTTTTT
1 CTAGTATTTCTTTGGTATTTTT
19375756 ATTGGTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.09, C:0.09, G:0.20, T:0.62
Consensus pattern (23 bp):
CTAGTATTTCTTTGGTATTTTTG
Found at i:19375749 original size:99 final size:98
Alignment explanation
Indices: 19375602--19375841 Score: 327
Period size: 99 Copynumber: 2.4 Consensus size: 98
19375592 CACATAGTTT
* * *
19375602 GATAAATTTACTAGTATTTTTTTGGTATTTTTGTTGGTATTTCTTTGGTGTTTTTGCTAGTATTT
1 GATAAATTTACTAGTA-TTTTTTGGTATTTTTGCTAGTATTTCTTTGGTGTTTTTACTAGTATTT
19375667 ATTTCTTGATATTTTCTTGATGTGATTGTAGGGC
65 ATTTCTTGATATTTTCTTGATGTGATTGTAGGGC
* * *
19375701 GATAAATTTACTAGTATTTCTTTGGTATTTTTGCTAGTGTTTCTTTGGTGTTTTTATTGGTATTT
1 GATAAATTTACTAGTATTT-TTTGGTATTTTTGCTAGTATTTCTTTGGTGTTTTTACTAGTATTT
* * * * *
19375766 GTTTCTTTATATTTTTTTGGTGTGATTGTAGGTC
65 ATTTCTTGATATTTTCTTGATGTGATTGTAGGGC
* * *
19375800 GATAAATTTACTGGTATTTTTTGGATGTTTTTGCTAGAATTT
1 GATAAATTTACTAGTATTTTTTGG-TATTTTTGCTAGTATTT
19375842 ATTTACTGAT
Statistics
Matches: 124, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
98 8 0.06
99 116 0.94
ACGTcount: A:0.17, C:0.06, G:0.20, T:0.57
Consensus pattern (98 bp):
GATAAATTTACTAGTATTTTTTGGTATTTTTGCTAGTATTTCTTTGGTGTTTTTACTAGTATTTA
TTTCTTGATATTTTCTTGATGTGATTGTAGGGC
Found at i:19376414 original size:17 final size:17
Alignment explanation
Indices: 19376392--19376435 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
19376382 AAATAATATG
*
19376392 AGGCAATCTAAAAATAA
1 AGGCAATCTAAAAACAA
* *
19376409 AGGCAATCTTATAACAA
1 AGGCAATCTAAAAACAA
19376426 A-GCAATCTAA
1 AGGCAATCTAA
19376436 TGAATGTCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.52, C:0.16, G:0.11, T:0.20
Consensus pattern (17 bp):
AGGCAATCTAAAAACAA
Found at i:19380546 original size:32 final size:30
Alignment explanation
Indices: 19380510--19380575 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 30
19380500 CCTTACATTA
* *
19380510 TTATCTAATTTCTGTTATAATATTTTACTTTG
1 TTATCAAATTT-T-TTATAAGATTTTACTTTG
*
19380542 TTATCAAATTTTTTATAAGCTTTTACTTTG
1 TTATCAAATTTTTTATAAGATTTTACTTTG
19380572 TTAT
1 TTAT
19380576 AACCATGTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 20 0.65
31 1 0.03
32 10 0.32
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.59
Consensus pattern (30 bp):
TTATCAAATTTTTTATAAGATTTTACTTTG
Found at i:19387073 original size:6 final size:6
Alignment explanation
Indices: 19387062--19387111 Score: 66
Period size: 6 Copynumber: 8.2 Consensus size: 6
19387052 AAAACGAACA
*
19387062 TTTCTC TTTCTC TTTCTC TTTCTC TTTCT- TTATGTC TTTCTC TTTGCTC
1 TTTCTC TTTCTC TTTCTC TTTCTC TTTCTC TT-TCTC TTTCTC TTT-CTC
19387111 T
1 T
19387112 GCTTTGCTGG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
5 2 0.05
6 31 0.79
7 6 0.15
ACGTcount: A:0.02, C:0.28, G:0.04, T:0.66
Consensus pattern (6 bp):
TTTCTC
Found at i:19396801 original size:62 final size:61
Alignment explanation
Indices: 19396615--19396803 Score: 175
Period size: 62 Copynumber: 3.0 Consensus size: 61
19396605 ATAATTACTG
* * ** *
19396615 AAGGCGTTTGTTAATAACACACGCCTTCAATAATTTTCCTCTAAAAAATTTTGAAATTATTA
1 AAGGCGTTTCTT-ATAACAAACGCCTTCAATAATTTTTTTCTAAAATATTTTGAAATTATTA
* * * * * * **
19396677 AAGGCGTATTC-TACTAACAAATGTCTTCAATAATTCTTTT-TAAATTATCTTCATAAAAATTA
1 AAGGCGT-TTCTTA-TAACAAACGCCTTCAATAATTTTTTTCTAAAATATTTTGA-AATTATTA
* * *
19396739 AGGGCGTTTCTTGATAATAAACGCCTTCAATAATTTTTTTCTAAAATATTTTGAGATTATTA
1 AAGGCGTTTCTT-ATAACAAACGCCTTCAATAATTTTTTTCTAAAATATTTTGAAATTATTA
19396801 AAG
1 AAG
19396804 ACATCTTCTA
Statistics
Matches: 96, Mismatches: 25, Indels: 12
0.72 0.19 0.09
Matches are distributed among these distances:
61 13 0.14
62 70 0.73
63 13 0.14
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.40
Consensus pattern (61 bp):
AAGGCGTTTCTTATAACAAACGCCTTCAATAATTTTTTTCTAAAATATTTTGAAATTATTA
Found at i:19403628 original size:28 final size:28
Alignment explanation
Indices: 19403576--19403629 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
19403566 ATTTTGTCTA
*
19403576 CGATGATTTGAGTTCATCAATTTTTGCG
1 CGATGATTTGAGTTCATCAACTTTTGCG
*
19403604 CGATGATTTGAGTTCATCGACTTTTG
1 CGATGATTTGAGTTCATCAACTTTTG
19403630 TGCTTGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43
Consensus pattern (28 bp):
CGATGATTTGAGTTCATCAACTTTTGCG
Found at i:19406017 original size:12 final size:12
Alignment explanation
Indices: 19405988--19406028 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 12
19405978 AAATTTTTTT
19405988 TAAAA-AAATAA
1 TAAAATAAATAA
*
19405999 T-AAATAAATAG
1 TAAAATAAATAA
19406010 TAAAATAAATAA
1 TAAAATAAATAA
19406022 -AAAATAA
1 TAAAATAA
19406029 GAAAAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 3 0.12
11 14 0.54
12 9 0.35
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (12 bp):
TAAAATAAATAA
Found at i:19406033 original size:19 final size:20
Alignment explanation
Indices: 19405992--19406027 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
19405982 TTTTTTTAAA
19405992 AAAAT-AATAAATAAATAGT
1 AAAATAAATAAATAAATAGT
19406011 AAAATAAATAAA-AAATA
1 AAAATAAATAAATAAATA
19406028 AGAAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (20 bp):
AAAATAAATAAATAAATAGT
Found at i:19406034 original size:20 final size:19
Alignment explanation
Indices: 19405991--19406034 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
19405981 TTTTTTTTAA
19405991 AAAAATAATAAATAAATAG
1 AAAAATAATAAATAAATAG
*
19406010 TAAAATAAATAAA-AAATAAG
1 AAAAAT-AATAAATAAAT-AG
19406030 AAAAA
1 AAAAA
19406035 AATTTGTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (19 bp):
AAAAATAATAAATAAATAG
Found at i:19410331 original size:11 final size:11
Alignment explanation
Indices: 19410315--19410358 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
19410305 TATCATAAAT
19410315 AAAAAAAAAAG
1 AAAAAAAAAAG
*
19410326 AAAAAAAATAG
1 AAAAAAAAAAG
*
19410337 AAAAGCAAAAAG
1 AAAA-AAAAAAG
19410349 AAAGAAAAAA
1 AAA-AAAAAA
19410359 TGAATAATGT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 14 0.52
12 12 0.44
13 1 0.04
ACGTcount: A:0.84, C:0.02, G:0.11, T:0.02
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:19412786 original size:79 final size:81
Alignment explanation
Indices: 19412702--19412931 Score: 240
Period size: 79 Copynumber: 2.9 Consensus size: 81
19412692 AGTTTTCTCA
* * *
19412702 AAATCACTTGGTGGTGATATTAGAGTATATAAATTTGAATTTTGTTAAAGTCTCTC-GATGGTGA
1 AAATCACTTGGTGGTGATATTAGAGTATATAAATCTAAATTTTGTTAAAATCTCTCAG-TGGTGA
*
19412766 TATCCAAGCA-TTTT-C
65 TATCCAAGAACTTTTGC
*** ** * *
19412781 AAATCACTCAATATTGATATCT-GAGTATCTAAATCCAAATTTTGTTAAAATCTCTCAGTGGTGA
1 AAATCACTTGGTGGTGATAT-TAGAGTATATAAATCTAAATTTTGTTAAAATCTCTCAGTGGTGA
*
19412845 TAT--ATGAACTTTTGC
65 TATCCAAGAACTTTTGC
* * **
19412860 AAATCACTTGGTGGTGATA-TATGAGTATTTAAGTCTAAATTTCATTAAAATCTCTCAGTGGTGA
1 AAATCACTTGGTGGTGATATTA-GAGTATATAAATCTAAATTTTGTTAAAATCTCTCAGTGGTGA
19412924 TATCCAAG
65 TATCCAAG
19412932 TATCCAAGTT
Statistics
Matches: 120, Mismatches: 23, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
77 4 0.03
78 4 0.03
79 108 0.90
80 2 0.02
81 2 0.02
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.38
Consensus pattern (81 bp):
AAATCACTTGGTGGTGATATTAGAGTATATAAATCTAAATTTTGTTAAAATCTCTCAGTGGTGAT
ATCCAAGAACTTTTGC
Found at i:19413070 original size:32 final size:33
Alignment explanation
Indices: 19413027--19413119 Score: 136
Period size: 32 Copynumber: 2.8 Consensus size: 33
19413017 TGTCTGAATA
*
19413027 TCTTTAAAATTTCTCGATGGTGATATTCAAGCT
1 TCTTTAAAATTTCTTGATGGTGATATTCAAGCT
*
19413060 T-TTTAAAATTTCTTGATAGTGATATTCAAGCT
1 TCTTTAAAATTTCTTGATGGTGATATTCAAGCT
*
19413092 TCTTTGAAAATTT-TTAATGGTGATATTC
1 TCTTT-AAAATTTCTTGATGGTGATATTC
19413120 GAGATCTCTT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
32 30 0.56
33 17 0.31
34 7 0.13
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (33 bp):
TCTTTAAAATTTCTTGATGGTGATATTCAAGCT
Found at i:19414236 original size:47 final size:47
Alignment explanation
Indices: 19414089--19414234 Score: 170
Period size: 46 Copynumber: 3.1 Consensus size: 47
19414079 TTTGTGTTTT
* * * * * **
19414089 AGTTTTTAGA-TTTATTTTCAAAAGTTGTGAAGCCTATGATGAAAAA
1 AGTTTTTAGATTTTATTTTCAAAAGTTATGAAACCTCTAATGAGAGG
* *
19414135 AGCTTTTAGATTTTATTTTCAAAAGTTATGCAACCTCTAATGAGAGG
1 AGTTTTTAGATTTTATTTTCAAAAGTTATGAAACCTCTAATGAGAGG
* * *
19414182 AGTTTTTAGA-TTTATTTTTAAAAGTTATGAAACCTCTTATTAGAGG
1 AGTTTTTAGATTTTATTTTCAAAAGTTATGAAACCTCTAATGAGAGG
19414228 AGTTTTT
1 AGTTTTT
19414235 TACAAATTAA
Statistics
Matches: 85, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
46 48 0.56
47 37 0.44
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.42
Consensus pattern (47 bp):
AGTTTTTAGATTTTATTTTCAAAAGTTATGAAACCTCTAATGAGAGG
Found at i:19415130 original size:42 final size:42
Alignment explanation
Indices: 19415036--19415499 Score: 423
Period size: 42 Copynumber: 10.7 Consensus size: 42
19415026 TTCCTTGATA
* * *
19415036 GAGGCATTGCAACTTTTAGAAAATAAAATGCTCCCCCACAACT
1 GAGGCTTTGAAACTTTGA-AAAATAAAATGCTCCCCCACAACT
* *
19415079 GAGGCTTTGAAACTTTGGAAAAATAAAATGCT-CCCTACAATT
1 GAGGCTTTGAAACTTT-GAAAAATAAAATGCTCCCCCACAACT
* * *
19415121 GAGGTTTTGAAACTTTGAAAAATAAATTGCTCCCCCGCAACT
1 GAGGCTTTGAAACTTTGAAAAATAAAATGCTCCCCCACAACT
* * *
19415163 AAGGCTTTAAAACTTTAGAAAAATAAAATGCTCACCCACAACT
1 GAGGCTTTGAAACTTT-GAAAAATAAAATGCTCCCCCACAACT
* * * *
19415206 AATGCTTTGAAACTTTTGAAAAATAAAATGAGATACTCCACCATAACT
1 GAGGCTTTGAAAC-TTTGAAAAATAAAAT--G---CTCCCCCACAACT
* * * * * *
19415254 AAGGCTCTGAAACTTTGAAAAATAACATGTTCCCCTACAATT
1 GAGGCTTTGAAACTTTGAAAAATAAAATGCTCCCCCACAACT
* * *
19415296 GAGGGCTTTGAAACTTTTGAAAAATAAAATACTCCACCATAA-T
1 GA-GGCTTTGAAAC-TTTGAAAAATAAAATGCTCCCCCACAACT
* * *
19415339 CGAGGCTTTGGAACTTTGAAAAATAAAATGCTCCCCTACAAAT
1 -GAGGCTTTGAAACTTTGAAAAATAAAATGCTCCCCCACAACT
* * *
19415382 GAGGCTTT-AAATTTTTGAAAAATAAAATGAGATACTCCACCATAACT
1 GAGGCTTTGAAA-CTTTGAAAAATAAAAT--G---CTCCCCCACAACT
* * *
19415429 GAGGCTCTGAAACTTTGAAAAATAAAATGCTCCCCTACAAAT
1 GAGGCTTTGAAACTTTGAAAAATAAAATGCTCCCCCACAACT
*
19415471 GAGGCTTT-AAACTTTTGAATAATAAAATG
1 GAGGCTTTGAAAC-TTTGAAAAATAAAATG
19415500 AGATCATTCT
Statistics
Matches: 344, Mismatches: 56, Indels: 43
0.78 0.13 0.10
Matches are distributed among these distances:
41 20 0.06
42 129 0.38
43 95 0.28
44 28 0.08
45 3 0.01
47 45 0.13
48 24 0.07
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (42 bp):
GAGGCTTTGAAACTTTGAAAAATAAAATGCTCCCCCACAACT
Found at i:19415400 original size:175 final size:176
Alignment explanation
Indices: 19415066--19415498 Score: 592
Period size: 175 Copynumber: 2.5 Consensus size: 176
19415056 AAATAAAATG
* * * *
19415066 CTCCCCCACAACTGAGGCTTTGAAACTTTGGAAAAATAAAATGCT-CCCTACAATTGAGGTTTTG
1 CTCCACCATAACTGAGGCTCTGAAACTTT-GAAAAATAAAATGCTCCCCTACAATTGAGGCTTTG
* * * *
19415130 AAAC-TTTGAAAAATAAATTGCTCCCCCGCAACTAAGGCTTTAAAACTTTAGAAAAATAAAATGC
65 AAACTTTTGAAAAATAAAATACTCCACCACAACTAAGGCTTTAAAACTTTAGAAAAATAAAATGC
* *
19415194 TCACCCACAACTAATGCTTTGAAACTTTTGAAAAATAAAATGAGATA
130 TCACCCACAAATAAGGCTTTGAAACTTTTGAAAAATAAAATGAGATA
* * *
19415241 CTCCACCATAACTAAGGCTCTGAAACTTTGAAAAATAACATGTTCCCCTACAATTGAGGGCTTTG
1 CTCCACCATAACTGAGGCTCTGAAACTTTGAAAAATAAAATGCTCCCCTACAATTGA-GGCTTTG
* * **
19415306 AAACTTTTGAAAAATAAAATACTCCACCATAA-TCGAGGCTTTGGAACTTT-GAAAAATAAAATG
65 AAACTTTTGAAAAATAAAATACTCCACCACAACT-AAGGCTTTAAAACTTTAGAAAAATAAAATG
* *
19415369 CTC-CCCTACAAATGAGGCTTT-AAATTTTTGAAAAATAAAATGAGATA
129 CTCACCC-ACAAATAAGGCTTTGAAACTTTTGAAAAATAAAATGAGATA
*
19415416 CTCCACCATAACTGAGGCTCTGAAACTTTGAAAAATAAAATGCTCCCCTACAAATGAGGCTTT-A
1 CTCCACCATAACTGAGGCTCTGAAACTTTGAAAAATAAAATGCTCCCCTACAATTGAGGCTTTGA
*
19415480 AACTTTTGAATAATAAAAT
66 AACTTTTGAAAAATAAAAT
19415499 GAGATCATTC
Statistics
Matches: 229, Mismatches: 24, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
173 19 0.08
174 19 0.08
175 118 0.52
176 38 0.17
177 35 0.15
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.27
Consensus pattern (176 bp):
CTCCACCATAACTGAGGCTCTGAAACTTTGAAAAATAAAATGCTCCCCTACAATTGAGGCTTTGA
AACTTTTGAAAAATAAAATACTCCACCACAACTAAGGCTTTAAAACTTTAGAAAAATAAAATGCT
CACCCACAAATAAGGCTTTGAAACTTTTGAAAAATAAAATGAGATA
Found at i:19415409 original size:47 final size:45
Alignment explanation
Indices: 19415358--19415498 Score: 130
Period size: 47 Copynumber: 3.1 Consensus size: 45
19415348 GGAACTTTGA
19415358 AAAATAAAATGCTCCCCTACAAATGAGGCTTTAAATTTTTGAAAAAT
1 AAAATAAAATGCTCCCCTACAAATGAGGCTTTAAA-TTTTG-AAAAT
* * * * * * *
19415405 AAAATGAGATACTCCACC-ATAACTGAGGCTCTGAAACTTTG---A-
1 AAAATAAAATGCTCC-CCTACAAATGAGGCT-TTAAATTTTGAAAAT
19415447 AAAATAAAATGCTCCCCTACAAATGAGGCTTTAAACTTTTGAATAAT
1 AAAATAAAATGCTCCCCTACAAATGAGGCTTTAAA-TTTTGAA-AAT
19415494 AAAAT
1 AAAAT
19415499 GAGATCATTC
Statistics
Matches: 71, Mismatches: 14, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
41 6 0.08
42 26 0.37
43 1 0.01
46 1 0.01
47 31 0.44
48 6 0.08
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.28
Consensus pattern (45 bp):
AAAATAAAATGCTCCCCTACAAATGAGGCTTTAAATTTTGAAAAT
Found at i:19415443 original size:89 final size:90
Alignment explanation
Indices: 19415066--19415503 Score: 521
Period size: 89 Copynumber: 5.0 Consensus size: 90
19415056 AAATAAAATG
* * * *
19415066 CTCCCCCACAACTGAGGCTTTGAAACTTTGGAAAAATAAAATGCT-CCCTACAATTGAGGTTTTG
1 CTCCACCATAACTGAGGCTTTGAAACTTT-GAAAAATAAAATGCTCCCCTACAAATGAGGCTTTG
*
19415130 AAAC-TTTGAAAAAT-AAAT----TG
65 AAACTTTTGAAAAATAAAATGAGATA
* ** * * * * *
19415150 CTCCCCCGCAACTAAGGCTTTAAAACTTTAGAAAAATAAAATGCTCACCC-ACAACTAATGCTTT
1 CTCCACCATAACTGAGGCTTTGAAACTTT-GAAAAATAAAATGCTC-CCCTACAAATGAGGCTTT
19415214 GAAACTTTTGAAAAATAAAATGAGATA
64 GAAACTTTTGAAAAATAAAATGAGATA
* * * * *
19415241 CTCCACCATAACTAAGGCTCTGAAACTTTGAAAAATAACATGTTCCCCTACAATTGAGGGCTTTG
1 CTCCACCATAACTGAGGCTTTGAAACTTTGAAAAATAAAATGCTCCCCTACAAATGA-GGCTTTG
19415306 AAACTTTTGAAAAAT--AA--A-ATA
65 AAACTTTTGAAAAATAAAATGAGATA
*
19415327 CTCCACCATAA-TCGAGGCTTTGGAACTTTGAAAAATAAAATGCTCCCCTACAAATGAGGCTTT-
1 CTCCACCATAACT-GAGGCTTTGAAACTTTGAAAAATAAAATGCTCCCCTACAAATGAGGCTTTG
*
19415390 AAATTTTTGAAAAATAAAATGAGATA
65 AAACTTTTGAAAAATAAAATGAGATA
*
19415416 CTCCACCATAACTGAGGCTCTGAAACTTTGAAAAATAAAATGCTCCCCTACAAATGAGGCTTT-A
1 CTCCACCATAACTGAGGCTTTGAAACTTTGAAAAATAAAATGCTCCCCTACAAATGAGGCTTTGA
*
19415480 AACTTTTGAATAATAAAATGAGAT
66 AACTTTTGAAAAATAAAATGAGAT
19415504 CATTCTTACC
Statistics
Matches: 307, Mismatches: 30, Indels: 29
0.84 0.08 0.08
Matches are distributed among these distances:
84 55 0.18
85 22 0.07
86 67 0.22
87 5 0.02
88 1 0.00
89 90 0.29
90 21 0.07
91 46 0.15
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.27
Consensus pattern (90 bp):
CTCCACCATAACTGAGGCTTTGAAACTTTGAAAAATAAAATGCTCCCCTACAAATGAGGCTTTGA
AACTTTTGAAAAATAAAATGAGATA
Found at i:19423375 original size:25 final size:25
Alignment explanation
Indices: 19423331--19423381 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
19423321 CTCTTTTGAC
* *
19423331 TAAAAAATTTAAACAAAAATTAAAT
1 TAAAAAATTAAAACAAAAATAAAAT
* *
19423356 TAAAAAATTAAAATACAAATAAAAT
1 TAAAAAATTAAAACAAAAATAAAAT
19423381 T
1 T
19423382 TAAGGCTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (25 bp):
TAAAAAATTAAAACAAAAATAAAAT
Found at i:19424180 original size:13 final size:13
Alignment explanation
Indices: 19424162--19424199 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
19424152 AAAATCTCAA
19424162 AAAACCCTAAACC
1 AAAACCCTAAACC
19424175 AAAACCCTAAAAACC
1 AAAACCCT--AAACC
19424190 -AAACCCTAAA
1 AAAACCCTAAA
19424200 TTCAAAACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 3 0.13
13 8 0.35
14 7 0.30
15 5 0.22
ACGTcount: A:0.58, C:0.34, G:0.00, T:0.08
Consensus pattern (13 bp):
AAAACCCTAAACC
Found at i:19424193 original size:14 final size:15
Alignment explanation
Indices: 19424162--19424199 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
19424152 AAAATCTCAA
19424162 AAAACCCT--AAACC
1 AAAACCCTAAAAACC
19424175 AAAACCCTAAAAACC
1 AAAACCCTAAAAACC
19424190 -AAACCCTAAA
1 AAAACCCTAAA
19424200 TTCAAAACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.35
14 10 0.43
15 5 0.22
ACGTcount: A:0.58, C:0.34, G:0.00, T:0.08
Consensus pattern (15 bp):
AAAACCCTAAAAACC
Found at i:19424236 original size:7 final size:6
Alignment explanation
Indices: 19424215--19424328 Score: 65
Period size: 7 Copynumber: 18.3 Consensus size: 6
19424205 AACCAAAATT
* *
19424215 TAAACC T-AGCC TAAATCC TAAACCC TAAACC T-AGCC TAAATCC TAAACCC
1 TAAACC TAAACC TAAA-CC TAAA-CC TAAACC TAAACC TAAA-CC TAAA-CC
* * * *
19424265 TAAACC T-AGCC TTAACAC TAAACCC TAAACC T-AGCC TAATCCC TAAACC
1 TAAACC TAAACC TAAAC-C TAAA-CC TAAACC TAAACC TAA-ACC TAAACC
*
19424314 AAAACC TAAAACC TA
1 TAAACC T-AAACC TA
19424329 GTCAAGCCCT
Statistics
Matches: 84, Mismatches: 14, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
5 16 0.19
6 23 0.27
7 44 0.52
8 1 0.01
ACGTcount: A:0.42, C:0.35, G:0.04, T:0.19
Consensus pattern (6 bp):
TAAACC
Found at i:19424243 original size:25 final size:25
Alignment explanation
Indices: 19424215--19424321 Score: 157
Period size: 25 Copynumber: 4.3 Consensus size: 25
19424205 AACCAAAATT
19424215 TAAACCTAGCCTAAATCCTAAACCC
1 TAAACCTAGCCTAAATCCTAAACCC
19424240 TAAACCTAGCCTAAATCCTAAACCC
1 TAAACCTAGCCTAAATCCTAAACCC
*
19424265 TAAACCTAGCCTTAA-CACTAAACCC
1 TAAACCTAGCCTAAATC-CTAAACCC
19424290 TAAACCTAGCCT-AATCCCTAAA-CC
1 TAAACCTAGCCTAAAT-CCTAAACCC
*
19424314 AAAACCTA
1 TAAACCTA
19424322 AAACCTAGTC
Statistics
Matches: 77, Mismatches: 2, Indels: 7
0.90 0.02 0.08
Matches are distributed among these distances:
24 12 0.16
25 64 0.83
26 1 0.01
ACGTcount: A:0.41, C:0.36, G:0.04, T:0.20
Consensus pattern (25 bp):
TAAACCTAGCCTAAATCCTAAACCC
Found at i:19424303 original size:18 final size:18
Alignment explanation
Indices: 19424231--19424313 Score: 70
Period size: 18 Copynumber: 4.8 Consensus size: 18
19424221 TAGCCTAAAT
19424231 CCTAAACCCTAAACCTAG
1 CCTAAACCCTAAACCTAG
*
19424249 CCTAAATCCTAAA-C---
1 CCTAAACCCTAAACCTAG
* *
19424263 CCTAAA-CCT-AGCCTTAA
1 CCTAAACCCTAAACC-TAG
19424280 CACTAAACCCTAAACCTAG
1 C-CTAAACCCTAAACCTAG
*
19424299 CCTAATCCCTAAACC
1 CCTAAACCCTAAACC
19424314 AAAACCTAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
12 1 0.02
13 4 0.08
14 6 0.12
17 2 0.04
18 30 0.58
19 6 0.12
20 3 0.06
ACGTcount: A:0.39, C:0.39, G:0.04, T:0.19
Consensus pattern (18 bp):
CCTAAACCCTAAACCTAG
Found at i:19424341 original size:18 final size:18
Alignment explanation
Indices: 19424313--19424358 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
19424303 ATCCCTAAAC
* *
19424313 CAAAACCTAAAACCTAGT
1 CAAACCCTAAAACCTACT
* *
19424331 CAAGCCCTAAACCCTACT
1 CAAACCCTAAAACCTACT
19424349 CAAACCCTAA
1 CAAACCCTAA
19424359 CCTAGACCCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.43, C:0.37, G:0.04, T:0.15
Consensus pattern (18 bp):
CAAACCCTAAAACCTACT
Found at i:19427534 original size:6 final size:6
Alignment explanation
Indices: 19427525--19427549 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19427515 ATAAAAAATA
19427525 AAATGC AAATGC AAATGC AAATGC A
1 AAATGC AAATGC AAATGC AAATGC A
19427550 TGAATAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
AAATGC
Found at i:19427620 original size:14 final size:14
Alignment explanation
Indices: 19427603--19427656 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
19427593 AGGTTTAAGG
*
19427603 TTTAGGGTTTCAAA
1 TTTAAGGTTTCAAA
* *
19427617 TTTAAAGTTT-AGCA
1 TTTAAGGTTTCA-AA
*
19427631 TTTAGGGTTTCAAA
1 TTTAAGGTTTCAAA
19427645 TTTAAGGTTTCA
1 TTTAAGGTTTCA
19427657 TGGAAAAATG
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
13 1 0.03
14 29 0.94
15 1 0.03
ACGTcount: A:0.30, C:0.07, G:0.19, T:0.44
Consensus pattern (14 bp):
TTTAAGGTTTCAAA
Found at i:19428572 original size:22 final size:21
Alignment explanation
Indices: 19428547--19428590 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
19428537 GAAAACCAAT
19428547 ATGAAAATGTAATAAAAATGCA
1 ATGAAAATGTAAT-AAAATGCA
*
19428569 ATGAAAATGTAATGAAATGCA
1 ATGAAAATGTAATAAAATGCA
19428590 A
1 A
19428591 AAAAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.57, C:0.05, G:0.16, T:0.23
Consensus pattern (21 bp):
ATGAAAATGTAATAAAATGCA
Found at i:19428582 original size:11 final size:11
Alignment explanation
Indices: 19428547--19428585 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
19428537 GAAAACCAAT
19428547 ATGAAAATGTA
1 ATGAAAATGTA
* *
19428558 ATAAAAATGCA
1 ATGAAAATGTA
19428569 ATGAAAATGTA
1 ATGAAAATGTA
19428580 ATGAAA
1 ATGAAA
19428586 TGCAAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.59, C:0.03, G:0.15, T:0.23
Consensus pattern (11 bp):
ATGAAAATGTA
Found at i:19428597 original size:22 final size:22
Alignment explanation
Indices: 19428550--19428596 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
19428540 AACCAATATG
**
19428550 AAAATGTAATAAAAATGCAATG
1 AAAATGTAATAAAAATGCAAAA
*
19428572 AAAATGTAAT-GAAATGCAAAA
1 AAAATGTAATAAAAATGCAAAA
19428593 AAAA
1 AAAA
19428597 AAATAGGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.64, C:0.04, G:0.13, T:0.19
Consensus pattern (22 bp):
AAAATGTAATAAAAATGCAAAA
Found at i:19428644 original size:16 final size:15
Alignment explanation
Indices: 19428623--19428652 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
19428613 TCCTCCAAGC
19428623 TTTTTTCAATTTTTTA
1 TTTTTTC-ATTTTTTA
19428639 TTTTTTCATTTTTT
1 TTTTTTCATTTTTT
19428653 TCTCTCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTCATTTTTTA
Found at i:19428671 original size:9 final size:9
Alignment explanation
Indices: 19428623--19428671 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
19428613 TCCTCCAAGC
*
19428623 TTTTTTCAA
1 TTTTTTCAT
19428632 TTTTTT-A-
1 TTTTTTCAT
19428639 TTTTTTCAT
1 TTTTTTCAT
19428648 TTTTTTC-T
1 TTTTTTCAT
*
19428656 CTCTTTTCAT
1 -TTTTTTCAT
19428666 TTTTTT
1 TTTTTT
19428672 TTCTTAACTT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
7 6 0.18
8 3 0.09
9 24 0.71
10 1 0.03
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTTCAT
Found at i:19428676 original size:16 final size:16
Alignment explanation
Indices: 19428625--19428676 Score: 61
Period size: 18 Copynumber: 3.1 Consensus size: 16
19428615 CTCCAAGCTT
*
19428625 TTTTCAATTTTTTATT-
1 TTTTC-ATTTTTTTTTC
19428641 TTTTCATTTTTTTCTCTC
1 TTTTCATTTTTTT-T-TC
19428659 TTTTCATTTTTTTTTC
1 TTTTCATTTTTTTTTC
19428675 TT
1 TT
19428677 AACTTCCTCC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 7 0.22
16 10 0.31
17 2 0.06
18 13 0.41
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTCATTTTTTTTTC
Found at i:19430163 original size:22 final size:22
Alignment explanation
Indices: 19430138--19430219 Score: 83
Period size: 22 Copynumber: 3.7 Consensus size: 22
19430128 TTATGTTCAA
*
19430138 AGGACTTTGAGATTATGTTTGG
1 AGGACTTTGAGATTATGCTTGG
* * * *
19430160 AGGATTTTGAAATTGTGCTTAG
1 AGGACTTTGAGATTATGCTTGG
* * * *
19430182 ATGACTTTAAGATTGTGCCTGG
1 AGGACTTTGAGATTATGCTTGG
19430204 AGGACTTTGAGATTAT
1 AGGACTTTGAGATTAT
19430220 TCAAAAATCT
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.26, C:0.07, G:0.28, T:0.39
Consensus pattern (22 bp):
AGGACTTTGAGATTATGCTTGG
Found at i:19430266 original size:40 final size:41
Alignment explanation
Indices: 19430234--19430360 Score: 148
Period size: 41 Copynumber: 3.1 Consensus size: 41
19430224 AAATCTAAGG
*
19430234 TTTTGCCTAAAGGTC-TTGAAAATTTTTTAAAAATTAAAAA
1 TTTTGCCTAAAGGTCTTTGAAAATGTTTTAAAAATTAAAAA
*
19430274 TTTTGCCTAAAGGTCTTTGGAAATGTTTTAAAAATTAAAAA
1 TTTTGCCTAAAGGTCTTTGAAAATGTTTTAAAAATTAAAAA
** * ** * * * *
19430315 TTTCACTTGGAGGTATTTGAAAATCTTTCAAAAATTTAAAA
1 TTTTGCCTAAAGGTCTTTGAAAATGTTTTAAAAATTAAAAA
19430356 TTTTG
1 TTTTG
19430361 TTTGAAGGTC
Statistics
Matches: 72, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
40 15 0.21
41 57 0.79
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.41
Consensus pattern (41 bp):
TTTTGCCTAAAGGTCTTTGAAAATGTTTTAAAAATTAAAAA
Found at i:19430393 original size:40 final size:40
Alignment explanation
Indices: 19430259--19430679 Score: 203
Period size: 40 Copynumber: 10.4 Consensus size: 40
19430249 TTGAAAATTT
* * * * * **
19430259 TTTAAAAATTAAAAATTTTGCCTAAAGGTCTTTGGAAATGT
1 TTTAAAATTTTAAAATTTTGCTTGAAGGTC-TTAGAAATCA
* * ** * * *
19430300 TTTAAAAATTAAAAATTTCACTTGGAGGTATTTGAAAATC-
1 TTTAAAATTTTAAAATTTTGCTTGAAGGTCTTAG-AAATCA
* *
19430340 TTTCAAAAATTTAAAATTTTGTTTGAAGGTCTTAGAAATCA
1 TTT-AAAATTTTAAAATTTTGCTTGAAGGTCTTAGAAATCA
* * * * *
19430381 TTTAAAATTTTAAGATTTTTCTTGAAGGTATTGGAAACCA
1 TTTAAAATTTTAAAATTTTGCTTGAAGGTCTTAGAAATCA
** * *
19430421 TTTAAAATTTTAAGGTTTTGCTTGAAGGT-TTTGAAATCG
1 TTTAAAATTTTAAAATTTTGCTTGAAGGTCTTAGAAATCA
* * * *
19430460 TTCAAAAATTTTAAAA-TTTGCTCGGAGGTCTTAGAGATCA
1 TT-TAAAATTTTAAAATTTTGCTTGAAGGTCTTAGAAATCA
* * * *
19430500 TTCAAAGA-TTTAAGATTTTGCTTGTAA-GTCTTTAGGAATTA
1 TTTAAA-ATTTTAAAATTTTGCTTG-AAGGTC-TTAGAAATCA
* * * * *
19430541 TTTAAAAATCTAAAGTTTTG-TCGGAA-GTCTTTGGAAATCA
1 TTTAAAATTTTAAAATTTTGCT-TGAAGGTC-TTAGAAATCA
* * * * * *
19430581 TTTAAAAATTTGATACTTTGCTTGGAGTTCTT-GAAAATTC-
1 TTTAAAATTTTAAAATTTTGCTTGAAGGTCTTAG-AAA-TCA
* * * * *
19430621 TTCAAAATTTTAAGATTTTACCTAAAGGTCTTTAGAAATCA
1 TTTAAAATTTTAAAATTTTGCTTGAAGGTC-TTAGAAATCA
* * *
19430662 TTCAAAAATCTAAAATTT
1 TTTAAAATTTTAAAATTT
19430680 AGCCCAGAGG
Statistics
Matches: 291, Mismatches: 71, Indels: 36
0.73 0.18 0.09
Matches are distributed among these distances:
39 30 0.10
40 157 0.54
41 103 0.35
42 1 0.00
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (40 bp):
TTTAAAATTTTAAAATTTTGCTTGAAGGTCTTAGAAATCA
Found at i:19430771 original size:21 final size:22
Alignment explanation
Indices: 19430745--19430789 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
19430735 AGTTTGAAAT
*
19430745 CTTTTCGCTT-CAAAATTTTCA
1 CTTTTCACTTACAAAATTTTCA
* *
19430766 CTTTTCATTTAGAAAATTTTCA
1 CTTTTCACTTACAAAATTTTCA
19430788 CT
1 CT
19430790 CTTTAACATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.27, C:0.20, G:0.04, T:0.49
Consensus pattern (22 bp):
CTTTTCACTTACAAAATTTTCA
Found at i:19433212 original size:20 final size:20
Alignment explanation
Indices: 19433172--19433231 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
19433162 AAAAAAAAAA
19433172 TTTCTTTT--TTTTTTTCATT
1 TTTCTTTTGCTTTTTTTC-TT
19433191 TTTGC-TTTGCTTTTTTTCTT
1 TTT-CTTTTGCTTTTTTTCTT
* *
19433211 TTTCTTTTTCTTTTTCTCTT
1 TTTCTTTTGCTTTTTTTCTT
19433231 T
1 T
19433232 CTTTCCTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
19 7 0.20
20 20 0.57
21 8 0.23
ACGTcount: A:0.02, C:0.15, G:0.03, T:0.80
Consensus pattern (20 bp):
TTTCTTTTGCTTTTTTTCTT
Found at i:19433242 original size:6 final size:6
Alignment explanation
Indices: 19433172--19433235 Score: 67
Period size: 6 Copynumber: 10.2 Consensus size: 6
19433162 AAAAAAAAAA
*
19433172 TTTCTT TTTTTT TTTCATT TTTGCTT TGCTT-TT TTTCTT TTTCTT TTTCTT
1 TTTCTT TTTCTT TTTC-TT TTT-CTT T--TTCTT TTTCTT TTTCTT TTTCTT
*
19433223 TTTCTC TTTCTT T
1 TTTCTT TTTCTT T
19433236 CCTTTTCATT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
5 2 0.04
6 33 0.67
7 11 0.22
8 1 0.02
9 2 0.04
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.80
Consensus pattern (6 bp):
TTTCTT
Found at i:19440268 original size:9 final size:9
Alignment explanation
Indices: 19440255--19440334 Score: 54
Period size: 9 Copynumber: 8.4 Consensus size: 9
19440245 TCGATTTTTC
19440255 TTTTTT-TT
1 TTTTTTATT
*
19440263 TGTTTTATT
1 TTTTTTATT
19440272 TTTTTTATT
1 TTTTTTATT
*
19440281 TTTTAATATGT
1 TTTT-TTAT-T
*
19440292 TTTTGGTATT
1 TTTT-TTATT
*
19440302 TTGTATTATT
1 TT-TTTTATT
**
19440312 TTTGGTATT
1 TTTTTTATT
19440321 TTTTTGTATT
1 TTTTT-TATT
19440331 TTTT
1 TTTT
19440335 ATTTTGTATT
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
8 5 0.09
9 22 0.39
10 20 0.36
11 9 0.16
ACGTcount: A:0.12, C:0.00, G:0.10, T:0.78
Consensus pattern (9 bp):
TTTTTTATT
Found at i:19440301 original size:21 final size:19
Alignment explanation
Indices: 19440265--19440333 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 19
19440255 TTTTTTTTTG
19440265 TTTTATT-TTTTT--TATT
1 TTTTATTATTTTTGGTATT
*
19440281 TTTTAATATGTTTTTGGTATT
1 TTTT-AT-TATTTTTGGTATT
*
19440302 TTGTATTATTTTTGGTATT
1 TTTTATTATTTTTGGTATT
19440321 TTTT-TGTATTTTT
1 TTTTAT-TATTTTT
19440334 TATTTTGTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
16 4 0.09
17 2 0.05
18 2 0.05
19 27 0.61
20 2 0.05
21 7 0.16
ACGTcount: A:0.14, C:0.00, G:0.10, T:0.75
Consensus pattern (19 bp):
TTTTATTATTTTTGGTATT
Found at i:19440341 original size:14 final size:14
Alignment explanation
Indices: 19440322--19440348 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19440312 TTTGGTATTT
19440322 TTTTGTATTTTTTA
1 TTTTGTATTTTTTA
19440336 TTTTGTATTTTTT
1 TTTTGTATTTTTT
19440349 GTCTGGATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.11, C:0.00, G:0.07, T:0.81
Consensus pattern (14 bp):
TTTTGTATTTTTTA
Found at i:19440348 original size:9 final size:9
Alignment explanation
Indices: 19440268--19440350 Score: 50
Period size: 10 Copynumber: 9.1 Consensus size: 9
19440258 TTTTTTGTTT
*
19440268 TATTTTTTT
1 TATTTTTTG
*
19440277 TATTTTTTAA
1 TATTTTTT-G
19440287 TATGTTTTTGG
1 TAT-TTTTT-G
19440298 TATTTTGTAT-
1 TATTTT-T-TG
*
19440308 TATTTTTGG
1 TATTTTTTG
19440317 TATTTTTTTG
1 TA-TTTTTTG
19440327 TA-TTTTT-
1 TATTTTTTG
19440334 TA--TTTTG
1 TATTTTTTG
19440341 TATTTTTTG
1 TATTTTTTG
19440350 T
1 T
19440351 CTGGATAAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
6 4 0.07
7 4 0.07
8 5 0.08
9 17 0.28
10 20 0.33
11 9 0.15
12 1 0.02
ACGTcount: A:0.14, C:0.00, G:0.11, T:0.75
Consensus pattern (9 bp):
TATTTTTTG
Found at i:19440595 original size:52 final size:50
Alignment explanation
Indices: 19440538--19440854 Score: 253
Period size: 49 Copynumber: 6.5 Consensus size: 50
19440528 CCTCTCACTT
* * ** *
19440538 GAGGCTCGATAACTTTTGAAATTTTAAAATCTGAAAAAGACTTATCTCAGCA
1 GAGGCTCAACAACTTTAAAAATTTT--AATCTGAAAAAGACTCATCTCAGCA
* * * *
19440590 GAGGCTCAACAACTTTAAAAATTTTATTTTGAAAAGGGCTCATCTCAGCA
1 GAGGCTCAACAACTTTAAAAATTTTAATCTGAAAAAGACTCATCTCAGCA
* * * * **
19440640 GAGGCTCCACAACTTTAAAAA-TCTCATCTTGGAAAAG-CTCATCTCAATA
1 GAGGCTCAACAACTTTAAAAATTTTAATC-TGAAAAAGACTCATCTCAGCA
** * *
19440689 GAGGCTCAACAAC-TTAAAAA--TCCATCTTAAAAAG-CTCCTCTCAGCA
1 GAGGCTCAACAACTTTAAAAATTTTAATCTGAAAAAGACTCATCTCAGCA
* * * * * *
19440735 AAGGCTCAACAACTTT-AAAA-TCTCATCTTGAAAAGGGCTCCTCTCAGCA
1 GAGGCTCAACAACTTTAAAAATTTTAATC-TGAAAAAGACTCATCTCAGCA
* *
19440784 GAGGCTCAACAACTTT-AAAA-TCTCATCTTGAAAAAG-CTTC-TCTCAGCA
1 GAGGCTCAACAACTTTAAAAATTTTAATC-TGAAAAAGAC-TCATCTCAGCA
19440832 GAGGCTCAACAACTTTAAAAATT
1 GAGGCTCAACAACTTTAAAAATT
19440855 CTCATCTTTT
Statistics
Matches: 224, Mismatches: 33, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
46 31 0.14
47 10 0.04
48 38 0.17
49 77 0.34
50 47 0.21
52 21 0.09
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (50 bp):
GAGGCTCAACAACTTTAAAAATTTTAATCTGAAAAAGACTCATCTCAGCA
Found at i:19440701 original size:49 final size:49
Alignment explanation
Indices: 19440582--19440895 Score: 381
Period size: 49 Copynumber: 6.4 Consensus size: 49
19440572 AAAAGACTTA
* * * *
19440582 TCTCAGCAGAGGCTCAACAACTTTAAAAATTTTAT-TTTGAAAAGGGCTCA
1 TCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTGGAAAA--GCTCC
* *
19440632 TCTCAGCAGAGGCTCCACAACTTTAAAAATCTCATCTTGGAAAAGCTCA
1 TCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTGGAAAAGCTCC
** *
19440681 TCTCAATAGAGGCTCAACAAC-TTAAAAATC-CATCTT-AAAAAGCTCC
1 TCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTGGAAAAGCTCC
*
19440727 TCTCAGCAAAGGCTCAACAACTTT-AAAATCTCATCTT-GAAAAGGGCTCC
1 TCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTGGAAAA--GCTCC
* *
19440776 TCTCAGCAGAGGCTCAACAACTTT-AAAATCTCATCTTGAAAAAGCTTC
1 TCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTGGAAAAGCTCC
19440824 TCTCAGCAGAGGCTCAACAACTTTAAAAATTCTCATCTTTTGGAAAAGCTCC
1 TCTCAGCAGAGGCTCAACAACTTTAAAAA-TCTCATC--TTGGAAAAGCTCC
* * *
19440876 TCTCAACAAAGGTTCAACAA
1 TCTCAGCAGAGGCTCAACAA
19440896 TGGAGTAGAG
Statistics
Matches: 233, Mismatches: 21, Indels: 18
0.86 0.08 0.07
Matches are distributed among these distances:
46 32 0.14
47 18 0.08
48 37 0.16
49 68 0.29
50 43 0.18
51 7 0.03
52 28 0.12
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (49 bp):
TCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTGGAAAAGCTCC
Found at i:19440750 original size:95 final size:96
Alignment explanation
Indices: 19440582--19441126 Score: 391
Period size: 99 Copynumber: 5.4 Consensus size: 96
19440572 AAAAGACTTA
* ** * * *
19440582 TCTCAGCAGAGGCTCAACAACTTTAAAAATTTTATTTTGAAAAGGGCTCATCTCAGCAGAGGCTC
1 TCTCAACAGAGGCTCAACAAC-TTAAAAA-TCCATCTTGAAAA-AGCTCCTCTCAGCAGAGGCTC
* *
19440647 CACAACTTTAAAAATCTCATCTTGGAAAAGCTCA
63 AACAACTTTAAAAATCTCATCTTGGAAAAGCTCC
* *
19440681 TCTCAATAGAGGCTCAACAACTTAAAAATCCATCTT-AAAAAGCTCCTCTCAGCAAAGGCTCAAC
1 TCTCAACAGAGGCTCAACAACTTAAAAATCCATCTTGAAAAAGCTCCTCTCAGCAGAGGCTCAAC
19440745 AACTTT-AAAATCTCATCTT-GAAAAGGGCTCC
66 AACTTTAAAAATCTCATCTTGGAAAA--GCTCC
* * *
19440776 TCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTGAAAAAGCTTCTCTCAGCAGAGGCTCAA
1 TCTCAACAGAGGCTCAACAACTTAAAAATC-CATCTTGAAAAAGCTCCTCTCAGCAGAGGCTCAA
19440841 CAACTTTAAAAATTCTCATCTTTTGGAAAAGCTCC
65 CAACTTTAAAAA-TCTCATC--TTGGAAAAGCTCC
* * ** *
19440876 TCTCAACAAAGGTTCAACAA-TGGAGTAGAGGCTCAACAACTTTAAAAATCATCTTGAAAAAGCT
1 TCTCAACAGAGGCTCAACAACT----T--A-----AA-AA---TCCAT-----CTTGAAAAAGCT
* * * * ** **
19440940 CCTCTCAACAAAGGGTCAACAAATTTAAAAATCTCATCTTACAAAAGCTAA
46 CCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTGGAAAAGCTCC
* * * * * *
19440991 TCTCAGCAGAGGCTCAACGACTTTAAAAATTCTCATCTTGAAAAAGGCTCATCTTAGCAAAGACT
1 TCTCAACAGAGGCTCAACAAC-TTAAAAA-TC-CATCTTGAAAAA-GCTCCTCTCAGCAGAGGCT
** * *
19441056 CAATGACTTTAAAAA--TCATCTTTTGAAAAGCTTC
62 CAACAACTTTAAAAATCTCATC-TTGGAAAAGCTCC
* *
19441090 TCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTT
1 TCTCAACAGAGGCTCAACAACTTAAAAATC-CATCTT
19441127 TTCTCAAAAT
Statistics
Matches: 360, Mismatches: 52, Indels: 70
0.75 0.11 0.15
Matches are distributed among these distances:
93 5 0.01
94 13 0.04
95 57 0.16
96 10 0.03
97 46 0.13
98 22 0.06
99 65 0.18
100 48 0.13
101 2 0.01
102 5 0.01
103 3 0.01
104 1 0.00
105 2 0.01
106 2 0.01
110 2 0.01
111 3 0.01
113 2 0.01
114 1 0.00
115 25 0.07
117 8 0.02
118 38 0.11
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (96 bp):
TCTCAACAGAGGCTCAACAACTTAAAAATCCATCTTGAAAAAGCTCCTCTCAGCAGAGGCTCAAC
AACTTTAAAAATCTCATCTTGGAAAAGCTCC
Found at i:19440959 original size:66 final size:68
Alignment explanation
Indices: 19440831--19440961 Score: 203
Period size: 66 Copynumber: 1.9 Consensus size: 68
19440821 TTCTCTCAGC
* *
19440831 AGAGGCTCAACAACTTTAAAAATTCTCATCTTTTGGAAAAGCTCCTCTCAACAAAGGTTCAACAA
1 AGAGGCTCAACAACTTTAAAAA-T-TCATC-TTTGAAAAAGCTCCTCTCAACAAAGGGTCAACAA
19440896 TGGAGT
63 TGGAGT
19440902 AGAGGCTCAACAACTTTAAAAA-TCATC-TTGAAAAAGCTCCTCTCAACAAAGGGTCAACAA
1 AGAGGCTCAACAACTTTAAAAATTCATCTTTGAAAAAGCTCCTCTCAACAAAGGGTCAACAA
19440962 ATTTAAAAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
66 31 0.53
68 5 0.09
71 22 0.38
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.24
Consensus pattern (68 bp):
AGAGGCTCAACAACTTTAAAAATTCATCTTTGAAAAAGCTCCTCTCAACAAAGGGTCAACAATGG
AGT
Found at i:19440995 original size:49 final size:49
Alignment explanation
Indices: 19440904--19441126 Score: 206
Period size: 49 Copynumber: 4.6 Consensus size: 49
19440894 AATGGAGTAG
**
19440904 AGGCTCAACAACTTTAAAAA--TCATCTTGAAAAAGCTCCTCTCAACAA
1 AGGCTCAACAACTTTAAAAATCTCATCTTGAAAAAGCTAATCTCAACAA
* * * *
19440951 AGGGTCAACAAATTTAAAAATCTCATCTT-ACAAAAGCTAATCTCAGCAG
1 AGGCTCAACAACTTTAAAAATCTCATCTTGA-AAAAGCTAATCTCAACAA
* * * *
19441000 AGGCTCAACGACTTTAAAAATTCTCATCTTGAAAAAGGCTCATCTTAGCAA
1 AGGCTCAACAACTTTAAAAA-TCTCATCTTGAAAAA-GCTAATCTCAACAA
* ** * ** * *
19441051 AGACTCAATGACTTTAAAAATCATC-TTTTG-AAAAGCTTCTCTCAGCAG
1 AGGCTCAACAACTTTAAAAATC-TCATCTTGAAAAAGCTAATCTCAACAA
19441099 AGGCTCAACAACTTT-AAAATCTCATCTT
1 AGGCTCAACAACTTTAAAAATCTCATCTT
19441127 TTCTCAAAAT
Statistics
Matches: 145, Mismatches: 23, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
46 2 0.01
47 27 0.19
48 23 0.16
49 42 0.29
50 19 0.13
51 32 0.22
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.27
Consensus pattern (49 bp):
AGGCTCAACAACTTTAAAAATCTCATCTTGAAAAAGCTAATCTCAACAA
Found at i:19441077 original size:215 final size:211
Alignment explanation
Indices: 19440687--19441109 Score: 568
Period size: 215 Copynumber: 2.0 Consensus size: 211
19440677 CTCATCTCAA
* *
19440687 TAGAGGCTCAACAACTTAAAAATCCATCTTAAAAAGCTCCTCTCAGCAAAGGCTCAACAACTTTA
1 TAGAGGCTCAACAACTTAAAAATCCATCTTAAAAAGCTCCTCTCAACAAAGGCTCAACAAATTTA
* **
19440752 AAATCTCATCTTGAAAAGGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTGAAA
66 AAATCTCATCTTGAAAAGAGCTAATCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTGAAA
* *
19440817 AAGCTTCTCTCAGCAGAGGCTCAACAACTTTAAAAATTCTCATCTTTTGGAAAAGCTCCTCTCAA
131 AAGCTTCTCTCAGCAAAGACTCAACAACTTTAAAAA-T-TCATCTTTT-GAAAAGCTCCTCTCAA
*
19440882 CAAAGGTTCAACAATGGAG
193 CAAAGGCTCAACAATGGAG
*
19440901 TAGAGGCTCAACAACTTTAAAAAT-CATCTTGAAAAAGCTCCTCTCAACAAAGGGTCAACAAATT
1 TAGAGGCTCAACAAC-TTAAAAATCCATCTT-AAAAAGCTCCTCTCAACAAAGGCTCAACAAATT
*
19440965 TAAAAATCTCATCTT-ACAAA-AGCTAATCTCAGCAGAGGCTCAACGACTTTAAAAATTCTCATC
64 T-AAAATCTCATCTTGA-AAAGAGCTAATCTCAGCAGAGGCTCAACAACTTT-AAAA-TCTCATC
* ** *
19441028 TTGAAAAAGGC-TCATCTTAGCAAAGACTCAATGACTTTAAAAA-TCATCTTTTGAAAAGCTTCT
125 TTGAAAAA-GCTTC-TCTCAGCAAAGACTCAACAACTTTAAAAATTCATCTTTTGAAAAGCTCCT
* *
19441091 CTCAGCAGAGGCTCAACAA
188 CTCAACAAAGGCTCAACAA
19441110 CTTTAAAATC
Statistics
Matches: 185, Mismatches: 16, Indels: 16
0.85 0.07 0.07
Matches are distributed among these distances:
214 47 0.25
215 75 0.41
216 20 0.11
217 17 0.09
218 26 0.14
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (211 bp):
TAGAGGCTCAACAACTTAAAAATCCATCTTAAAAAGCTCCTCTCAACAAAGGCTCAACAAATTTA
AAATCTCATCTTGAAAAGAGCTAATCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTGAAA
AAGCTTCTCTCAGCAAAGACTCAACAACTTTAAAAATTCATCTTTTGAAAAGCTCCTCTCAACAA
AGGCTCAACAATGGAG
Found at i:19441110 original size:266 final size:260
Alignment explanation
Indices: 19440639--19441128 Score: 698
Period size: 266 Copynumber: 1.9 Consensus size: 260
19440629 TCATCTCAGC
* * * *
19440639 AGAGGCTCCACAACTTTAAAAATCTCATCTTGGAAAAGCTCATCTCAATAGAGGCTCAACAACTT
1 AGAGGCTCAACAACTTTAAAAA-CTCATCTTGAAAAAGCTCATCTCAACAAAGGCTCAACAACTT
**
19440704 AAAAATCCATCTTAAAAAGCTCCTCTCAGCAAAGGCTCAACAACTTTAAAATCTCATCTTGAAAA
65 AAAAATCCATCTTAAAAAGCTAATCTCAGCAAAGGCTCAACAACTTTAAAATCTCATCTTGAAAA
* * * *
19440769 GGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTGAAAAAGCTTCTCTCAGCAGA
130 AGGCTCATCTCAGCAAAGACTCAACAACTTTAAAATCTCATCTTGAAAAAGCTTCTCTCAGCAGA
19440834 GGCTCAACAACTTTAAAAATTCTCATCTTTTGGAAAAGCTCCTCTCAACAAAGGTTCAACAATGG
195 GGCTCAACAACTTT-AAAA-TCTCATCTTTTGGAAAAGCTCCTCTCAACAAAGGTTCAACAATGG
19440899 AGT
258 AGT
* * *
19440902 AGAGGCTCAACAACTTTAAAAA-TCATCTTGAAAAAGCTCCTCTCAACAAAGGGTCAACAAATTT
1 AGAGGCTCAACAACTTTAAAAACTCATCTTGAAAAAGCTCATCTCAACAAAGGCTCAAC-AACTT
* *
19440966 AAAAATCTCATCTTACAAAAGCTAATCTCAGCAGAGGCTCAACGACTTTAAAAATTCTCATCTTG
65 AAAAATC-CATCTTA-AAAAGCTAATCTCAGCAAAGGCTCAACAACTTT-AAAA-TCTCATCTTG
* ** *
19441031 AAAAAGGCTCATCTTAGCAAAGACTCAATGACTTTAAAAATCATC-TTTTG-AAAAGCTTCTCTC
126 AAAAAGGCTCATCTCAGCAAAGACTCAACAACTTT-AAAATC-TCATCTTGAAAAAGCTTCTCTC
19441094 AGCAGAGGCTCAACAACTTTAAAATCTCATCTTTT
189 AGCAGAGGCTCAACAACTTTAAAATCTCATCTTTT
19441129 CTCAAAATTG
Statistics
Matches: 201, Mismatches: 19, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
261 31 0.15
262 11 0.05
263 28 0.14
264 40 0.20
265 8 0.04
266 71 0.35
267 10 0.05
268 2 0.01
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (260 bp):
AGAGGCTCAACAACTTTAAAAACTCATCTTGAAAAAGCTCATCTCAACAAAGGCTCAACAACTTA
AAAATCCATCTTAAAAAGCTAATCTCAGCAAAGGCTCAACAACTTTAAAATCTCATCTTGAAAAA
GGCTCATCTCAGCAAAGACTCAACAACTTTAAAATCTCATCTTGAAAAAGCTTCTCTCAGCAGAG
GCTCAACAACTTTAAAATCTCATCTTTTGGAAAAGCTCCTCTCAACAAAGGTTCAACAATGGAGT
Found at i:19451693 original size:17 final size:17
Alignment explanation
Indices: 19451659--19451716 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 17
19451649 AAAAAAACAT
**
19451659 TTTTTA-TTTTTTAATG
1 TTTTTATTTTTTTTGTG
19451675 TTTTTATTTTTTTTGTG
1 TTTTTATTTTTTTTGTG
* **
19451692 TTTTGAGATTTTTTGT-
1 TTTTTATTTTTTTTGTG
19451708 TTTTT-TTTT
1 TTTTTATTTT
19451717 ATTACGCATA
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
15 2 0.06
16 10 0.30
17 21 0.64
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.79
Consensus pattern (17 bp):
TTTTTATTTTTTTTGTG
Found at i:19451695 original size:26 final size:25
Alignment explanation
Indices: 19451658--19451714 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
19451648 AAAAAAAACA
*
19451658 TTTTTTATTTTTTA-ATGTTTTTATT
1 TTTTTTATTTTTGAGAT-TTTTTATT
* *
19451683 TTTTTTGTGTTTTGAGATTTTTTGTT
1 TTTTTTAT-TTTTGAGATTTTTTATT
19451709 TTTTTT
1 TTTTTT
19451715 TTATTACGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 7 0.26
26 18 0.67
27 2 0.07
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.79
Consensus pattern (25 bp):
TTTTTTATTTTTGAGATTTTTTATT
Found at i:19454602 original size:24 final size:22
Alignment explanation
Indices: 19454568--19454616 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 22
19454558 TTTTTTTGTA
19454568 TTTTGTATTAT-TTTTGGTATTT
1 TTTTGTATTATATTTT-GTATTT
19454590 TTTTGTATTTTATATTTTGTATTT
1 TTTTGTA--TTATATTTTGTATTT
19454614 TTT
1 TTT
19454617 ATCTGGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.29
24 13 0.54
25 4 0.17
ACGTcount: A:0.14, C:0.00, G:0.10, T:0.76
Consensus pattern (22 bp):
TTTTGTATTATATTTTGTATTT
Found at i:19475328 original size:22 final size:22
Alignment explanation
Indices: 19475293--19475343 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
19475283 AAAGGGGATT
*
19475293 AAAAAGAAACAGAAACA-AAAG
1 AAAAAAAAACAGAAACAGAAAG
*
19475314 AAAAAAAAACAAGAAATAGAAAG
1 AAAAAAAAAC-AGAAACAGAAAG
19475337 AAAAAAA
1 AAAAAAA
19475344 TGAAAGCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 9 0.35
22 6 0.23
23 11 0.42
ACGTcount: A:0.80, C:0.06, G:0.12, T:0.02
Consensus pattern (22 bp):
AAAAAAAAACAGAAACAGAAAG
Found at i:19475837 original size:20 final size:19
Alignment explanation
Indices: 19475793--19475847 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
19475783 GAATCCACTT
19475793 AAAGAAAAAGAAAGGAAAA
1 AAAGAAAAAGAAAGGAAAA
19475812 AGAAGAAAAAGAAAGTGAAAGA
1 A-AAGAAAAAGAAAG-GAAA-A
*
19475834 AAGAGGAAAAGAAA
1 AA-AGAAAAAGAAA
19475848 AAGTAAAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 1 0.03
20 13 0.42
21 5 0.16
22 12 0.39
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (19 bp):
AAAGAAAAAGAAAGGAAAA
Found at i:19482307 original size:43 final size:44
Alignment explanation
Indices: 19482259--19482426 Score: 146
Period size: 43 Copynumber: 3.8 Consensus size: 44
19482249 CATAGTGGCA
19482259 ATATCCGAGTGTTCAAAGTTC-AAGCTTTTAAATCTCGATGGTG
1 ATATCCGAGTGTTCAAAGTTCAAAGCTTTTAAATCTCGATGGTG
* * * *
19482302 ATATCCGAGTATTCAAAAATTCAAATTTCATTTAAATCTCGATGGTG
1 ATATCCGAGTGTTC-AAAGTTCAAA--GCTTTTAAATCTCGATGGTG
* ** * * *
19482349 ACATTTGAGTGTTCAAAG-TCTAAG-TTTTCAAAGCTTGATGGTG
1 ATATCCGAGTGTTCAAAGTTCAAAGCTTTT-AAATCTCGATGGTG
** * *
19482392 ATATTTGAGTGTTCAAAGTCCAAA-TTTTTAAATCT
1 ATATCCGAGTGTTCAAAGTTCAAAGCTTTTAAATCT
19482427 TAGTAGTGAT
Statistics
Matches: 100, Mismatches: 18, Indels: 14
0.76 0.14 0.11
Matches are distributed among these distances:
42 3 0.03
43 47 0.47
44 13 0.13
45 6 0.06
46 3 0.03
47 28 0.28
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.38
Consensus pattern (44 bp):
ATATCCGAGTGTTCAAAGTTCAAAGCTTTTAAATCTCGATGGTG
Found at i:19482436 original size:43 final size:43
Alignment explanation
Indices: 19482346--19482443 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 43
19482336 AATCTCGATG
* * * *
19482346 GTGACATTTGAGTGTTCAAAGTCTAAGTTTTCAAAGCTTGATG
1 GTGATATTTGAGTGTTCAAAGTCCAAATTTTCAAAGCTTGATA
* *
19482389 GTGATATTTGAGTGTTCAAAGTCCAAATTTTTAAATCTT-AGTA
1 GTGATATTTGAGTGTTCAAAGTCCAAATTTTCAAAGCTTGA-TA
19482432 GTGAT-TTTGAGT
1 GTGATATTTGAGT
19482444 TTTTATCATA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 8 0.17
43 40 0.83
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (43 bp):
GTGATATTTGAGTGTTCAAAGTCCAAATTTTCAAAGCTTGATA
Found at i:19482817 original size:23 final size:24
Alignment explanation
Indices: 19482786--19482832 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
19482776 AGCTTTTATC
*
19482786 AAAATTCTTTT-GATAGTGATATT
1 AAAAGTCTTTTCGATAGTGATATT
19482809 AAAAGTCTTTTCGATAGTGATATT
1 AAAAGTCTTTTCGATAGTGATATT
19482833 TGGGAACTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.34, C:0.06, G:0.15, T:0.45
Consensus pattern (24 bp):
AAAAGTCTTTTCGATAGTGATATT
Found at i:19482960 original size:116 final size:117
Alignment explanation
Indices: 19482825--19483036 Score: 293
Period size: 116 Copynumber: 1.8 Consensus size: 117
19482815 CTTTTCGATA
* * *
19482825 GTGATATTTGGGAACTTTTTAGTGGCAATATTCGTAGTCATTTTGAATTCTCCTTAGTGGTGATA
1 GTGATATTTGGAAACTTTTTAGTGGCAATATTCGAAGTCATTTTGAATTCTCCTTAGTGATGATA
* * *
19482890 TCCGAGAACCA-TTCAA-TGGTGATATTTGAAGGCATTTGCATTTTCTCGGTG
66 TCC-AAAAACATTTCAAGTGGTGATATCTGAAGGCATTTGCATTTTCTCGGTG
* ** * * *
19482941 GTGATATTTGGAAAGTTTTTTTTGGCAATATTTGAAGTCATTTTGCATTTTCCTTAGTGATGATA
1 GTGATATTTGGAAACTTTTTAGTGGCAATATTCGAAGTCATTTTGAATTCTCCTTAGTGATGATA
19483006 TCCAAAAACATTTCAAGTGGTGATATCTGAA
66 TCCAAAAACATTTCAAGTGGTGATATCTGAA
19483037 ATTATCTTGC
Statistics
Matches: 82, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
115 5 0.06
116 64 0.78
117 13 0.16
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (117 bp):
GTGATATTTGGAAACTTTTTAGTGGCAATATTCGAAGTCATTTTGAATTCTCCTTAGTGATGATA
TCCAAAAACATTTCAAGTGGTGATATCTGAAGGCATTTGCATTTTCTCGGTG
Found at i:19483299 original size:9 final size:9
Alignment explanation
Indices: 19483285--19483350 Score: 64
Period size: 9 Copynumber: 7.4 Consensus size: 9
19483275 AAAAGGTAAT
19483285 AAAAATTCA
1 AAAAATTCA
*
19483294 AAAAATCCA
1 AAAAATTCA
*
19483303 AAAAATTTA
1 AAAAATTCA
19483312 AAAAATTC-
1 AAAAATTCA
*
19483320 ATAAA-TCAA
1 AAAAATTC-A
*
19483329 AAAAAATCA
1 AAAAATTCA
*
19483338 AAAAGTTCA
1 AAAAATTCA
19483347 AAAA
1 AAAA
19483351 TCCATAACAA
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
7 2 0.04
8 4 0.09
9 38 0.83
10 2 0.04
ACGTcount: A:0.68, C:0.11, G:0.02, T:0.20
Consensus pattern (9 bp):
AAAAATTCA
Found at i:19483325 original size:26 final size:26
Alignment explanation
Indices: 19483285--19483354 Score: 86
Period size: 26 Copynumber: 2.7 Consensus size: 26
19483275 AAAAGGTAAT
* *
19483285 AAAAATTCAAAAAATCCAAAAAATTTA
1 AAAAATTC-AAAAATCCAAAAAAATCA
* *
19483312 AAAAATTCATAAATCAAAAAAAATCA
1 AAAAATTCAAAAATCCAAAAAAATCA
*
19483338 AAAAGTTCAAAAATCCA
1 AAAAATTCAAAAATCCA
19483355 TAACAAAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
26 28 0.78
27 8 0.22
ACGTcount: A:0.66, C:0.13, G:0.01, T:0.20
Consensus pattern (26 bp):
AAAAATTCAAAAATCCAAAAAAATCA
Found at i:19483341 original size:34 final size:34
Alignment explanation
Indices: 19483293--19483364 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
19483283 ATAAAAATTC
* *
19483293 AAAAAATCCAAAAAATTTAAAAAATTCATAAATCAA
1 AAAAAATCCAAAAAAGTTAAAAAATCCAT-AA-CAA
*
19483329 AAAAAAT-C-AAAAAGTTCAAAAATCCATAACAA
1 AAAAAATCCAAAAAAGTTAAAAAATCCATAACAA
19483361 AAAA
1 AAAA
19483365 CTAAAAAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 7 0.21
33 2 0.06
34 16 0.48
35 1 0.03
36 7 0.21
ACGTcount: A:0.68, C:0.12, G:0.01, T:0.18
Consensus pattern (34 bp):
AAAAAATCCAAAAAAGTTAAAAAATCCATAACAA
Found at i:19484378 original size:26 final size:27
Alignment explanation
Indices: 19484349--19484399 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
19484339 TCGGTTTAAA
19484349 GTTTAGTTTAAGGTTT-AGGTTTTGGG
1 GTTTAGTTTAAGGTTTAAGGTTTTGGG
* **
19484375 GTTTGGTTTGGGGTTTAAGGTTTTG
1 GTTTAGTTTAAGGTTTAAGGTTTTG
19484400 TTTAGGGTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.12, C:0.00, G:0.37, T:0.51
Consensus pattern (27 bp):
GTTTAGTTTAAGGTTTAAGGTTTTGGG
Found at i:19484396 original size:14 final size:13
Alignment explanation
Indices: 19484360--19484397 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
19484350 TTTAGTTTAA
19484360 GGTTTAGGTTTTGG
1 GGTTTAGG-TTTGG
19484374 GGTTT-GGTTTGG
1 GGTTTAGGTTTGG
19484386 GGTTTAAGGTTT
1 GGTTT-AGGTTT
19484398 TGTTTAGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 10 0.45
13 2 0.09
14 10 0.45
ACGTcount: A:0.08, C:0.00, G:0.42, T:0.50
Consensus pattern (13 bp):
GGTTTAGGTTTGG
Found at i:19484479 original size:18 final size:18
Alignment explanation
Indices: 19484453--19484488 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19484443 GTTTAGTTCA
*
19484453 ATTTGGTTTAAGGTTTGG
1 ATTTAGTTTAAGGTTTGG
*
19484471 ATTTAGTTTAGGGTTTGG
1 ATTTAGTTTAAGGTTTGG
19484489 GGTTCGGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (18 bp):
ATTTAGTTTAAGGTTTGG
Found at i:19484492 original size:25 final size:25
Alignment explanation
Indices: 19484464--19484512 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
19484454 TTTGGTTTAA
*
19484464 GGTTTGGATT-TAGTTTAGGGTTTGG
1 GGTTCGGATTCTA-TTTAGGGTTTGG
*
19484489 GGTTCGGTTTCTATTTAGGGTTTG
1 GGTTCGGATTCTATTTAGGGTTTG
19484513 AGTTTTCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.10, C:0.04, G:0.37, T:0.49
Consensus pattern (25 bp):
GGTTCGGATTCTATTTAGGGTTTGG
Found at i:19484551 original size:7 final size:7
Alignment explanation
Indices: 19484539--19484658 Score: 64
Period size: 7 Copynumber: 18.7 Consensus size: 7
19484529 TCGGGTTAGC
19484539 TTTAGGG
1 TTTAGGG
19484546 TTTAGGG
1 TTTAGGG
*
19484553 TTAAGGG
1 TTTAGGG
19484560 TTT--GG
1 TTTAGGG
** *
19484565 CATGGGG
1 TTTAGGG
19484572 TTT--GG
1 TTTAGGG
*
19484577 TTTTGGG
1 TTTAGGG
*
19484584 TTTAAGG
1 TTTAGGG
19484591 TTTA-GG
1 TTTAGGG
19484597 TTTA--G
1 TTTAGGG
19484602 TTTAGGG
1 TTTAGGG
19484609 TTTAGGG
1 TTTAGGG
19484616 TTT--GG
1 TTTAGGG
*
19484621 TTTAAGG
1 TTTAGGG
*
19484628 TTT--TG
1 TTTAGGG
* *
19484633 TTTAAGT
1 TTTAGGG
*
19484640 TTTAGGA
1 TTTAGGG
19484647 TTTAGGG
1 TTTAGGG
19484654 TTTAG
1 TTTAG
19484659 AGATTAATGT
Statistics
Matches: 89, Mismatches: 14, Indels: 20
0.72 0.11 0.16
Matches are distributed among these distances:
5 22 0.25
6 6 0.07
7 61 0.69
ACGTcount: A:0.16, C:0.01, G:0.36, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:19484604 original size:25 final size:25
Alignment explanation
Indices: 19484570--19484651 Score: 80
Period size: 25 Copynumber: 3.3 Consensus size: 25
19484560 TTTGGCATGG
*
19484570 GGTTTGGTTTTGGGTTTAAGGTTTA
1 GGTTTAGTTTTGGGTTTAAGGTTTA
* *
19484595 GGTTTAGTTTAGGGTTTAGGGTTT-
1 GGTTTAGTTTTGGGTTTAAGGTTTA
*
19484619 GGTTTAAGGTTTT--GTTTAAGTTTTA
1 GGTTT-A-GTTTTGGGTTTAAGGTTTA
19484644 GGATTTAG
1 GG-TTTAG
19484652 GGTTTAGAGA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
24 15 0.32
25 25 0.53
26 7 0.15
ACGTcount: A:0.16, C:0.00, G:0.33, T:0.51
Consensus pattern (25 bp):
GGTTTAGTTTTGGGTTTAAGGTTTA
Found at i:19484636 original size:31 final size:31
Alignment explanation
Indices: 19484575--19484658 Score: 89
Period size: 31 Copynumber: 2.6 Consensus size: 31
19484565 CATGGGGTTT
* *
19484575 GGTTTTGGGTTTAAGGTTTAGGTTTAGTTTAG
1 GGTTTAGGGTTT-AGGTTTAGGTTTAGTTTAA
*
19484607 GGTTTAGGGTTT-GGTTTAAGGTTTTGTTTAA
1 GGTTTAGGGTTTAGGTTT-AGGTTTAGTTTAA
* *
19484638 GTTTTAGGATTTAGGGTTTAG
1 GGTTTAGGGTTTA-GGTTTAG
19484659 AGATTAATGT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
30 5 0.11
31 21 0.48
32 13 0.30
33 5 0.11
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (31 bp):
GGTTTAGGGTTTAGGTTTAGGTTTAGTTTAA
Found at i:19488719 original size:25 final size:24
Alignment explanation
Indices: 19488691--19488792 Score: 78
Period size: 20 Copynumber: 4.5 Consensus size: 24
19488681 AATAATATCT
19488691 TAAAAATATTATTATATTTATTATA
1 TAAAAATATTATTATA-TTATTATA
*
19488716 T--AAATAATATTATATTA--ATA
1 TAAAAATATTATTATATTATTATA
* *
19488736 -AATAATA-TATTATATTAATA-A
1 TAAAAATATTATTATATTATTATA
*
19488757 T-ACAATATTATT-TATTTATTAATA
1 TAAAAATATTATTATA-TTATT-ATA
19488781 TAAAAATATTAT
1 TAAAAATATTAT
19488793 CTATTAAGAA
Statistics
Matches: 62, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
20 13 0.21
21 12 0.19
22 12 0.19
23 13 0.21
24 2 0.03
25 10 0.16
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (24 bp):
TAAAAATATTATTATATTATTATA
Found at i:19488726 original size:23 final size:22
Alignment explanation
Indices: 19488694--19488792 Score: 82
Period size: 22 Copynumber: 4.5 Consensus size: 22
19488684 AATATCTTAA
* *
19488694 AAATATTATTATATTTATTATAT
1 AAATAATATTATA-TTAATATAT
*
19488717 AAATAATATTATATTAATAAAT
1 AAATAATATTATATTAATATAT
19488739 -AAT-ATATTATATTAATA-AT
1 AAATAATATTATATTAATATAT
* *
19488758 ACAATATTATT-TATTTATTAATAT
1 A-AATAATATTATA-TTAAT-ATAT
19488782 AAA-AATATTAT
1 AAATAATATTAT
19488793 CTATTAAGAA
Statistics
Matches: 63, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
19 2 0.03
20 14 0.22
21 8 0.13
22 20 0.32
23 16 0.25
24 3 0.05
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATAATATTATATTAATATAT
Found at i:19488747 original size:20 final size:19
Alignment explanation
Indices: 19488703--19489133 Score: 78
Period size: 18 Copynumber: 22.8 Consensus size: 19
19488693 AAAATATTAT
19488703 TATATT-TATTATATAAATA
1 TATATTATATTA-ATAAATA
19488722 -ATATTATATTAATAAATAA
1 TATATTATATTAATAAAT-A
*
19488741 TATATTATATTAATAATACAA
1 TATATTATATTAATAA-A-TA
19488762 TATTATTTATTTATTAATATAA-A
1 TA-TA-TTA--TATTAATA-AATA
* *
19488785 AATATTATCTATTAA-GAATA
1 TATATTA--TATTAATAAATA
* *
19488805 TATTATTCATA-TAATATATG
1 TA-TATT-ATATTAATAAATA
* * * * * *
19488825 TTTAATATAATATTTATTAA
1 TATATTATATTAATAAAT-A
* *
19488845 TATGTTATATGAATATAATA
1 TATATTATATTAATA-AATA
*
19488865 TATTATTATATGAAT--ATA
1 TA-TATTATATTAATAAATA
* *
19488883 -ATATT-TGTTAATATAT-
1 TATATTATATTAATAAATA
19488899 TA-ATGTATTATTAAT--ATA
1 TATAT-TA-TATTAATAAATA
*
19488917 -ATATT-TATTAATATAT-
1 TATATTATATTAATAAATA
19488933 TAT-TTATATTAAT--ATCA
1 TATATTATATTAATAAAT-A
* *
19488950 TATATTATTAGTAATATAAGA
1 TATATTA-TATTAATA-AATA
* *
19488971 GTATATTGCTAAT-ATAATATA
1 -TATATT-ATATTAATAA-ATA
*
19488992 TTATATTAT-TAATATAGTAATA
1 -TATATTATATTA-ATA--AATA
* *
19489014 AATATTATATTAAGAAATA
1 TATATTATATTAATAAATA
* * * *
19489033 -ATATAATATTATTTATTA
1 TATATTATATTAATAAATA
* *
19489051 -ATATAATATTTATAAATAA
1 TATATTATATTAATAAAT-A
*
19489070 TATATTA-ATAAATAAAT-
1 TATATTATATTAATAAATA
* *
19489087 TGTATTATATT--GAAA-A
1 TATATTATATTAATAAATA
*
19489103 TA-A-TATATTATTAAATA
1 TATATTATATTAATAAATA
19489120 T-TATTATATTAATA
1 TATATTATATTAATA
19489134 TTATTATATT
Statistics
Matches: 301, Mismatches: 57, Indels: 109
0.64 0.12 0.23
Matches are distributed among these distances:
14 6 0.02
15 15 0.05
16 15 0.05
17 32 0.11
18 59 0.20
19 43 0.14
20 40 0.13
21 55 0.18
22 20 0.07
23 6 0.02
25 9 0.03
26 1 0.00
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.48
Consensus pattern (19 bp):
TATATTATATTAATAAATA
Found at i:19488797 original size:25 final size:26
Alignment explanation
Indices: 19488743--19488798 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
19488733 ATAAATAATA
* *
19488743 TATTATATTAATAATACAATATTATT
1 TATTATATTAATAATAAAATATTATC
19488769 TATT-TATTAAT-ATAAAAATATTATC
1 TATTATATTAATAAT-AAAATATTATC
19488794 TATTA
1 TATTA
19488799 AGAATATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 2 0.08
25 20 0.77
26 4 0.15
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (26 bp):
TATTATATTAATAATAAAATATTATC
Found at i:19488885 original size:49 final size:49
Alignment explanation
Indices: 19488828--19488939 Score: 138
Period size: 49 Copynumber: 2.3 Consensus size: 49
19488818 ATATATGTTT
* *
19488828 AATATAATATTTATTAATATGTTATATG-AATA-TAATATATTATTATATG
1 AATATAATATTTATTAATATATTA-ATGTAATATTAATATAATATT-TATG
* * *
19488877 AATATAATATTTGTTAATATATTAATGTATTATTAATATAATATTTATT
1 AATATAATATTTATTAATATATTAATGTAATATTAATATAATATTTATG
*
19488926 AATATATTATTTAT
1 AATATAATATTTAT
19488940 ATTAATATCA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
48 3 0.06
49 40 0.74
50 11 0.20
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (49 bp):
AATATAATATTTATTAATATATTAATGTAATATTAATATAATATTTATG
Found at i:19488898 original size:23 final size:21
Alignment explanation
Indices: 19488850--19488916 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
19488840 ATTAATATGT
*
19488850 TATATGAATATAATATATTAT
1 TATATGAATATAATATATTAA
*
19488871 TATATGAATATAATATTTGTTAA
1 TATATGAATATAATA--TATTAA
* *
19488894 TATATTAATGT-AT-TATTAA
1 TATATGAATATAATATATTAA
19488913 TATA
1 TATA
19488917 ATATTTATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
19 9 0.23
21 15 0.38
22 2 0.05
23 13 0.33
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (21 bp):
TATATGAATATAATATATTAA
Found at i:19488927 original size:26 final size:27
Alignment explanation
Indices: 19488896--19488947 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
19488886 TTTGTTAATA
*
19488896 TATTAATGTATTATTAATA-TAATATT
1 TATTAATATATTATTAATATTAATATT
*
19488922 TATTAATATATTATTTATATTAATAT
1 TATTAATATATTATTAATATTAATAT
19488948 CATATATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (27 bp):
TATTAATATATTATTAATATTAATATT
Found at i:19489035 original size:51 final size:51
Alignment explanation
Indices: 19488980--19489084 Score: 135
Period size: 51 Copynumber: 2.1 Consensus size: 51
19488970 AGTATATTGC
*
19488980 TAATATAATA-TATTATATT-AT-TAATATAGTAATAAATATTATATTAAGAAA
1 TAATATAATATTATT-TATTAATATAATAT--TAATAAATAATATATTAAGAAA
* *
19489031 TAATATAATATTATTTATTAATATAATATTTATAAATAATATATTAATAAA
1 TAATATAATATTATTTATTAATATAATATTAATAAATAATATATTAAGAAA
19489082 TAA
1 TAA
19489085 ATTGTATTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
51 36 0.75
52 6 0.12
53 6 0.12
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (51 bp):
TAATATAATATTATTTATTAATATAATATTAATAAATAATATATTAAGAAA
Found at i:19489130 original size:8 final size:8
Alignment explanation
Indices: 19489106--19489147 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
19489096 TTGAAAATAA
19489106 TATATTAT
1 TATATTAT
19489114 TAAATATTAT
1 T--ATATTAT
19489124 TATATTA-
1 TATATTAT
19489131 -ATATTAT
1 TATATTAT
19489138 TATATTAT
1 TATATTAT
19489146 TA
1 TA
19489148 ATAACAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
6 6 0.20
8 16 0.53
10 8 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TATATTAT
Found at i:19489138 original size:14 final size:14
Alignment explanation
Indices: 19489103--19489144 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
19489093 ATATTGAAAA
19489103 TAATA-TATTAT-T
1 TAATATTATTATAT
*
19489115 AAATATTATTATAT
1 TAATATTATTATAT
19489129 TAATATTATTATAT
1 TAATATTATTATAT
19489143 TA
1 TA
19489145 TTAATAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 4 0.15
13 6 0.23
14 16 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TAATATTATTATAT
Found at i:19490413 original size:26 final size:25
Alignment explanation
Indices: 19490384--19490432 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
19490374 TAATATTCTT
19490384 AAATAAAGTTTTTTTGTAAAAAAATA
1 AAATAAA-TTTTTTTGTAAAAAAATA
* * *
19490410 AAATTAATTTTTTTTTCAAAAAA
1 AAATAAATTTTTTTGTAAAAAAA
19490433 GTTGAAAGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (25 bp):
AAATAAATTTTTTTGTAAAAAAATA
Found at i:19490606 original size:20 final size:21
Alignment explanation
Indices: 19490583--19490627 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
19490573 CTTAATTCTA
19490583 TTTTTAA-AAACC-AAAATAT
1 TTTTTAATAAACCTAAAATAT
* *
19490602 TTTTTAATAAACCTTAAATTT
1 TTTTTAATAAACCTAAAATAT
19490623 TTTTT
1 TTTTT
19490628 TATTTTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 7 0.32
20 5 0.23
21 10 0.45
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTTTAATAAACCTAAAATAT
Found at i:19491719 original size:16 final size:16
Alignment explanation
Indices: 19491675--19491731 Score: 82
Period size: 16 Copynumber: 3.6 Consensus size: 16
19491665 TGTATTCAAG
19491675 AATTTAAAATTATTTAA
1 AATTTAAAATTATTT-A
19491692 AATTT-AAA-TATTTA
1 AATTTAAAATTATTTA
*
19491706 AATTTAAAATTATTCA
1 AATTTAAAATTATTTA
19491722 AATTTAAAAT
1 AATTTAAAAT
19491732 GATCTTAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
14 6 0.16
15 8 0.22
16 18 0.49
17 5 0.14
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
AATTTAAAATTATTTA
Found at i:19493176 original size:21 final size:22
Alignment explanation
Indices: 19493142--19493185 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
19493132 TGTGTTTTAT
*
19493142 TATATGATAGAATAGGATAAGA
1 TATATGATAGAATAAGATAAGA
* *
19493164 TATATTAT-GAATAAGATTAGA
1 TATATGATAGAATAAGATAAGA
19493185 T
1 T
19493186 TAAATAATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.34
Consensus pattern (22 bp):
TATATGATAGAATAAGATAAGA
Found at i:19498761 original size:27 final size:28
Alignment explanation
Indices: 19498707--19498758 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
19498697 ACAAATTACT
* *
19498707 TTCAATATATTATATAATAAATAGAATA
1 TTCAATATATTACATAATAAATAAAATA
19498735 TTCAATA-ATTACATAA-AAATAAAA
1 TTCAATATATTACATAATAAATAAAA
19498759 ATAAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 7 0.32
27 8 0.36
28 7 0.32
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.35
Consensus pattern (28 bp):
TTCAATATATTACATAATAAATAAAATA
Found at i:19499062 original size:8 final size:9
Alignment explanation
Indices: 19499041--19499078 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
19499031 TTTTATCTAA
19499041 AAAAATTTT
1 AAAAATTTT
19499050 AAAAATTTT
1 AAAAATTTT
19499059 AAAAA--TT
1 AAAAATTTT
19499066 ACAAAATTTT
1 A-AAAATTTT
19499076 AAA
1 AAA
19499079 TTTATATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
7 3 0.12
8 4 0.15
9 16 0.62
10 3 0.12
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (9 bp):
AAAAATTTT
Found at i:19501679 original size:10 final size:10
Alignment explanation
Indices: 19501664--19501693 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
19501654 ATTGAATTTT
19501664 TATATTTTAA
1 TATATTTTAA
19501674 TATATTTTAA
1 TATATTTTAA
19501684 T-TATTTTAA
1 TATATTTTAA
19501693 T
1 T
19501694 TGATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:19502474 original size:2 final size:2
Alignment explanation
Indices: 19502467--19502495 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19502457 AGTGATCCCA
19502467 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
19502496 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:19502633 original size:45 final size:46
Alignment explanation
Indices: 19502563--19502650 Score: 126
Period size: 45 Copynumber: 1.9 Consensus size: 46
19502553 CAAGCTTAAA
* *
19502563 AAATTATTTTTGTTTTTTTAATTATCAT-TTTTA-AAATTTTATCT
1 AAATAATTTTTGTATTTTTAATTATCATCTTTTATAAATTTTATCT
19502607 AAATAATTTATTGTATTTTTAATTATCATCTTTTATTAAATTTT
1 AAATAATTT-TTGTATTTTTAATTATCATCTTTTA-TAAATTTT
19502651 GTTGAAAGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
44 8 0.21
45 18 0.47
46 5 0.13
48 7 0.18
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (46 bp):
AAATAATTTTTGTATTTTTAATTATCATCTTTTATAAATTTTATCT
Found at i:19502777 original size:139 final size:133
Alignment explanation
Indices: 19502572--19502848 Score: 365
Period size: 139 Copynumber: 2.0 Consensus size: 133
19502562 AAAATTATTT
* * * * * *
19502572 TTGTTTTTTTAATTATCATTTTTAAAATTTTATCTAAATAATTTATTGTATTTTTAATTATCATC
1 TTGTTTTCTTAATGACCATTTTTAAAATTTTATCTAAAGAAATTATTATATTTTTAATTATCATC
* * *
19502637 TTTTATTAAATTTTGTTGAAAGAACTGAATTATTGAGATCAATATGTATATATAGAATAAGTTTA
66 TTTTATTAAATTTTGTTGAAAAAACTGAATTATTGAAATC-A-A--TATATATACAATAAGTTTA
19502702 TTACTTA
127 TTACTTA
* * * *
19502709 TTGTTTTCTTAATGACCATTTTTATTAAATTTTGTTTAAAGAAATTGTTATATTTTTAATTATTA
1 TTGTTTTCTTAATGACCATTTTTA--AAATTTTATCTAAAGAAATTATTATATTTTTAATTATCA
*
19502774 TCTTTTATTAAATTTTGTTGAAAAAATTGAATTATTGAAATCAATATATATACAATAAGTTTATT
64 TCTTTTATTAAATTTTGTTGAAAAAACTGAATTATTGAAATCAATATATATACAATAAGTTTATT
*
19502839 GCTTA
129 ACTTA
19502844 TTGTT
1 TTGTT
19502849 ATTGACTAAT
Statistics
Matches: 123, Mismatches: 15, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
135 29 0.24
137 22 0.18
138 1 0.01
139 71 0.58
ACGTcount: A:0.35, C:0.05, G:0.08, T:0.52
Consensus pattern (133 bp):
TTGTTTTCTTAATGACCATTTTTAAAATTTTATCTAAAGAAATTATTATATTTTTAATTATCATC
TTTTATTAAATTTTGTTGAAAAAACTGAATTATTGAAATCAATATATATACAATAAGTTTATTAC
TTA
Found at i:19502891 original size:139 final size:137
Alignment explanation
Indices: 19502620--19502876 Score: 337
Period size: 139 Copynumber: 1.9 Consensus size: 137
19502610 TAATTTATTG
* *
19502620 TATTTTTAATTATCATCTTTTATTAAATTTTGTTGAAAGAACTGAATTATTGAGATCAATATGTA
1 TATTTTTAATTATCATCTTTTATTAAATTTTGTTGAAAAAACTGAATTATTGAAATCAATA-GTA
* * ** *
19502685 TATATAGAATAAGTTTATTACTTATTGTTTTCTTAATGACCATTTTTATTAAATTTTGTTTAAAG
65 TATATACAATAAGTTTATTACTTATTGTTTTCTTAATGA-CATTTATAAAAAAATTTGTTTAAAG
19502750 AAATTGTTA
129 AAATTGTTA
* *
19502759 TATTTTTAATTATTATCTTTTATTAAATTTTGTTGAAAAAATTGAATTATTGAAATC-A-A-TAT
1 TATTTTTAATTATCATCTTTTATTAAATTTTGTTGAAAAAACTGAATTATTGAAATCAATAGTAT
*
19502821 ATATACAATAAGTTTATTGCTTATTGTTATTGAC-TAATGA-A-TTATAAAAAAATTTG
66 ATATACAATAAGTTTATTACTTATTGTT-TT--CTTAATGACATTTATAAAAAAATTTG
19502877 AATTTGCAAT
Statistics
Matches: 105, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
134 11 0.10
135 30 0.29
136 2 0.02
137 7 0.07
138 2 0.02
139 53 0.50
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (137 bp):
TATTTTTAATTATCATCTTTTATTAAATTTTGTTGAAAAAACTGAATTATTGAAATCAATAGTAT
ATATACAATAAGTTTATTACTTATTGTTTTCTTAATGACATTTATAAAAAAATTTGTTTAAAGAA
ATTGTTA
Found at i:19503254 original size:20 final size:19
Alignment explanation
Indices: 19503203--19503257 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
19503193 ATTATTATAC
19503203 ATAAT-TTTTATATAAAAT
1 ATAATATTTTATATAAAAT
** *
19503221 ATAATATAAATATATAAATT
1 ATAATAT-TTTATATAAAAT
19503241 AATAATATTTTATATAA
1 -ATAATATTTTATATAA
19503258 TATAAAAACA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
18 5 0.17
19 1 0.03
20 16 0.55
21 7 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATAATATTTTATATAAAAT
Found at i:19509558 original size:11 final size:11
Alignment explanation
Indices: 19509530--19509561 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
19509520 ATATTTAGAA
*
19509530 TATATAATTGT
1 TATATAGTTGT
19509541 TATATAGTTGT
1 TATATAGTTGT
19509552 TATATAGTTG
1 TATATAGTTG
19509562 CATATTGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (11 bp):
TATATAGTTGT
Found at i:19513485 original size:6 final size:6
Alignment explanation
Indices: 19513476--19513513 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
19513466 ATATATGTAT
19513476 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC AT
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC AT
19513514 GTGTGCATGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:19517717 original size:24 final size:26
Alignment explanation
Indices: 19517681--19517728 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
19517671 GAACTCACCA
19517681 AAAATCATAAAAATATT-ATGAAATT
1 AAAATCATAAAAATATTCATGAAATT
*
19517706 AAAATC-TAAAAATTTTCATGAAA
1 AAAATCATAAAAATATTCATGAAA
19517729 ATCTAAGCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.31
Consensus pattern (26 bp):
AAAATCATAAAAATATTCATGAAATT
Found at i:19517725 original size:144 final size:145
Alignment explanation
Indices: 19517520--19517865 Score: 317
Period size: 144 Copynumber: 2.4 Consensus size: 145
19517510 TAGTCATGTT
* ** * * * * ** *
19517520 TATGATTTTAAA-GCATAAAAAATCATGAAATACTATAGAATTAAAATTTGGAA-AGTTTCATGA
1 TATGATTTTAAATACACCAAAAATCATAAAATATTATAAAATTAAAATCTAAAATATTTTCATGA
* * * *
19517583 AATTTTGACCTCAAAAAAGCCAAATTACAAAAATACCCC-TATAAGAGTAATTTGATAA-TTTCA
66 AAATCTAACCTCAAAAAAGCCAAATTACAAAAATACCCCTTACAAGAGTAATTTGATAATTTTCA
* * *
19517646 CTTTTTGGGGTATTGC
131 CCTTTT-GGGTACTAC
* *
19517662 TATGATTTTGAACT-CACCAAAAATCATAAAAATATTATGAAATTAAAATCTAAAA-ATTTTCAT
1 TATGATTTT-AAATACACCAAAAATCAT-AAAATATTATAAAATTAAAATCTAAAATATTTTCAT
* * ** * ** * ** *
19517725 GAAAATCTAAGCTCAGAAAAGTTAATTTATGAAAATACCCCTTACAAGGGTGTTTTGGTAATTTT
64 GAAAATCTAACCTCAAAAAAGCCAAATTACAAAAATACCCCTTACAAGAGTAATTTGATAATTTT
* *
19517790 GACCTTTTGGGTACTAT
129 CACCTTTTGGGTACTAC
* *
19517807 TGTGATTTTAAATACACCAAAAATCATAAAATATTATAAAATTAAGATCTAAAATATTT
1 TATGATTTTAAATACACCAAAAATCATAAAATATTATAAAATTAAAATCTAAAATATTT
19517866 CACAAAAATT
Statistics
Matches: 162, Mismatches: 35, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
142 9 0.06
143 13 0.08
144 86 0.53
145 45 0.28
146 9 0.06
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34
Consensus pattern (145 bp):
TATGATTTTAAATACACCAAAAATCATAAAATATTATAAAATTAAAATCTAAAATATTTTCATGA
AAATCTAACCTCAAAAAAGCCAAATTACAAAAATACCCCTTACAAGAGTAATTTGATAATTTTCA
CCTTTTGGGTACTAC
Found at i:19521791 original size:37 final size:36
Alignment explanation
Indices: 19521705--19521791 Score: 93
Period size: 37 Copynumber: 2.4 Consensus size: 36
19521695 ATTAAAAGGC
***
19521705 TAGGTTTAAGGTTTAGGGTTTTTTAAGCTTTTTGTT
1 TAGGTTTAAGGTTTAGGGTTTTTTAAGCTTAGGGTT
* * * *
19521741 TAGGATTAGGGTTTGGGGTATTTTTAAGGTTAGGGTT
1 TAGGTTTAAGGTTTAGGGT-TTTTTAAGCTTAGGGTT
*
19521778 TTGGTTTAAGGTTT
1 TAGGTTTAAGGTTT
19521792 TTTTATGGTT
Statistics
Matches: 40, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
36 16 0.40
37 24 0.60
ACGTcount: A:0.17, C:0.01, G:0.31, T:0.51
Consensus pattern (36 bp):
TAGGTTTAAGGTTTAGGGTTTTTTAAGCTTAGGGTT
Found at i:19524848 original size:120 final size:119
Alignment explanation
Indices: 19524682--19524987 Score: 305
Period size: 120 Copynumber: 2.5 Consensus size: 119
19524672 TACTCCGAAT
* *
19524682 CTTGAAAATCATTCACAAAATTTAAAACTCTATAC-GGAGATCTTGGAAATCGTTAAAAAATTTA
1 CTTGAAAATCATTCA-AAAATTTAAAA-T-TATGCTGGAGATCTTGGAAATCATTAAAAAATTTA
* * ** * * * *
19524746 AGATTCTATCTTGA-GGTCTTGAAAATCATTCAAGAGTTTAAAATTCTACCCTAAA-GA
63 AAATTCTA-CTTAATCATCATGAAAATAATTCAAAAATTTAAAATTCTACCC-AAAGGA
* * *
19524803 CTTGAAAATCATTCAAAAATTTAAAATTATGCTTGGAGATTTTGGAAATCATTCAAATATTTAAA
1 CTTGAAAATCATTCAAAAATTTAAAATTATGC-TGGAGATCTTGGAAATCATTAAAAAATTTAAA
* * *** *
19524868 ATTTTACTTAATCATCATGAAAATAATTCAAAAATTTAAAATTTTGTGCAAAGGT
65 ATTCTACTTAATCATCATGAAAATAATTCAAAAATTTAAAATTCTACCCAAAGGA
** * * *
19524923 CTTG-AAATCATTCAAAAATTTAAAATTATGCTCAAAAGTCTTGAAAATCATTTAAAAATTTAAA
1 CTTGAAAATCATTCAAAAATTTAAAATTATGCTGGAGA-TCTTGGAAATCATTAAAAAATTTAAA
19524987 A
65 A
19524988 ATTTTGTTCA
Statistics
Matches: 154, Mismatches: 26, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
118 7 0.05
119 58 0.38
120 74 0.48
121 15 0.10
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (119 bp):
CTTGAAAATCATTCAAAAATTTAAAATTATGCTGGAGATCTTGGAAATCATTAAAAAATTTAAAA
TTCTACTTAATCATCATGAAAATAATTCAAAAATTTAAAATTCTACCCAAAGGA
Done.